Author Archives: gene_x

Workflow using PICRUSt2 for Data_Karoline_16S_2025 (v2)

Leave a reply
  • Welchs_t-test
  • STAMP_Screenshot

  1. Environment Setup: It sets up a Conda environment named picrust2, using the conda create command and then activates this environment using conda activate picrust2.

    #https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.2.0-beta)#minimum-requirements-to-run-full-tutorial
mamba create -n picrust2 -c bioconda -c conda-forge picrust2    #2.5.3  #=2.2.0_b
mamba activate /home/jhuang/miniconda3/envs/picrust2

Under docker-env (qiime2-amplicon-2023.9)

  1. Export QIIME2 feature table and representative sequences

    #docker pull quay.io/qiime2/core:2023.9
#docker run -it --rm \
#-v /mnt/md1/DATA/Data_Karoline_16S_2025:/data \
#-v /home/jhuang/REFs:/home/jhuang/REFs \
#quay.io/qiime2/core:2023.9 bash
#cd /data
# === SETTINGS ===
FEATURE_TABLE_QZA="dada2_tests2/test_7_f240_r240/table.qza"
REP_SEQS_QZA="dada2_tests2/test_7_f240_r240/rep-seqs.qza"

# === STEP 1: EXPORT QIIME2 ARTIFACTS ===
mkdir -p qiime2_export
qiime tools export --input-path $FEATURE_TABLE_QZA --output-path qiime2_export
qiime tools export --input-path $REP_SEQS_QZA --output-path qiime2_export

  2. Convert BIOM to TSV for Picrust2 input

    biom convert \
-i qiime2_export/feature-table.biom \
-o qiime2_export/feature-table.tsv \
--to-tsv

Under env (picrust2): mamba activate /home/jhuang/miniconda3/envs/picrust2

  1. Run PICRUSt2 pipeline

    tail -n +2 qiime2_export/feature-table.tsv > qiime2_export/feature-table-fixed.tsv
picrust2_pipeline.py \
-s qiime2_export/dna-sequences.fasta \
-i qiime2_export/feature-table-fixed.tsv \
-o picrust2_out \
-p 100

#This will:
#* Place sequences in the reference tree (using EPA-NG),
#* Predict gene family abundances (e.g., EC, KO, PFAM, TIGRFAM),
#* Predict pathway abundances.

#In current PICRUSt2 (with picrust2_pipeline.py), you do not run hsp.py separately.
#Instead, picrust2_pipeline.py internally runs the HSP step for all functional categories automatically. It outputs all the prediction files (16S_predicted_and_nsti.tsv.gz, COG_predicted.tsv.gz, PFAM_predicted.tsv.gz, KO_predicted.tsv.gz, EC_predicted.tsv.gz, TIGRFAM_predicted.tsv.gz, PHENO_predicted.tsv.gz) in the output directory.

mkdir picrust2_out_advanced; cd picrust2_out_advanced
#If you still want to run hsp.py manually (advanced use / debugging), the commands correspond directly:
hsp.py -i 16S -t ../picrust2_out/out.tre -o 16S_predicted_and_nsti.tsv.gz -p 100 -n
hsp.py -i COG -t ../picrust2_out/out.tre -o COG_predicted.tsv.gz -p 100
hsp.py -i PFAM -t ../picrust2_out/out.tre -o PFAM_predicted.tsv.gz -p 100
hsp.py -i KO -t ../picrust2_out/out.tre -o KO_predicted.tsv.gz -p 100
hsp.py -i EC -t ../picrust2_out/out.tre -o EC_predicted.tsv.gz -p 100
hsp.py -i TIGRFAM -t ../picrust2_out/out.tre -o TIGRFAM_predicted.tsv.gz -p 100
hsp.py -i PHENO -t ../picrust2_out/out.tre -o PHENO_predicted.tsv.gz -p 100

  2. Metagenome prediction per functional category (if needed separately)

    #cd picrust2_out_advanced
metagenome_pipeline.py -i ../qiime2_export/feature-table.biom -m 16S_predicted_and_nsti.tsv.gz -f COG_predicted.tsv.gz -o COG_metagenome_out --strat_out
metagenome_pipeline.py -i ../qiime2_export/feature-table.biom -m 16S_predicted_and_nsti.tsv.gz -f EC_predicted.tsv.gz -o EC_metagenome_out --strat_out
metagenome_pipeline.py -i ../qiime2_export/feature-table.biom -m 16S_predicted_and_nsti.tsv.gz -f KO_predicted.tsv.gz -o KO_metagenome_out --strat_out
metagenome_pipeline.py -i ../qiime2_export/feature-table.biom -m 16S_predicted_and_nsti.tsv.gz -f PFAM_predicted.tsv.gz -o PFAM_metagenome_out --strat_out
metagenome_pipeline.py -i ../qiime2_export/feature-table.biom -m 16S_predicted_and_nsti.tsv.gz -f TIGRFAM_predicted.tsv.gz -o TIGRFAM_metagenome_out --strat_out

# Add descriptions in gene family tables
add_descriptions.py -i COG_metagenome_out/pred_metagenome_unstrat.tsv.gz -m COG -o COG_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz
add_descriptions.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC -o EC_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz
add_descriptions.py -i KO_metagenome_out/pred_metagenome_unstrat.tsv.gz -m KO -o KO_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz   # EC and METACYC is a pair, EC for gene_annotation and METACYC for pathway_annotation
add_descriptions.py -i PFAM_metagenome_out/pred_metagenome_unstrat.tsv.gz -m PFAM -o PFAM_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz
add_descriptions.py -i TIGRFAM_metagenome_out/pred_metagenome_unstrat.tsv.gz -m TIGRFAM -o TIGRFAM_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

  3. Pathway inference (MetaCyc pathways from EC numbers)

    #cd picrust2_out_advanced
pathway_pipeline.py -i EC_metagenome_out/pred_metagenome_contrib.tsv.gz -o EC_pathways_out -p 100
pathway_pipeline.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -o EC_pathways_out_per_seq -p 100 --per_sequence_contrib --per_sequence_abun EC_metagenome_out/seqtab_norm.tsv.gz --per_sequence_function EC_predicted.tsv.gz
#ERROR due to missing .../pathway_mapfiles/KEGG_pathways_to_KO.tsv
pathway_pipeline.py -i COG_metagenome_out/pred_metagenome_contrib.tsv.gz -o KEGG_pathways_out -p 100 --no_regroup --map /home/jhuang/anaconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv
pathway_pipeline.py -i KO_metagenome_out/pred_metagenome_strat.tsv.gz -o KEGG_pathways_out -p 100 --no_regroup --map /home/jhuang/anaconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv

add_descriptions.py -i EC_pathways_out/path_abun_unstrat.tsv.gz -m METACYC -o EC_pathways_out/path_abun_unstrat_descrip.tsv.gz
gunzip EC_pathways_out/path_abun_unstrat_descrip.tsv.gz

#Error - no rows remain after regrouping input table. The default pathway and regroup mapfiles are meant for EC numbers. Note that KEGG pathways are not supported since KEGG is a closed-source database, but you can input custom pathway mapfiles if you have access. If you are using a custom function database did you mean to set the --no-regroup flag and/or change the default pathways mapfile used?
#If ERROR --> USE the METACYC for downstream analyses!!!

#ERROR due to missing .../description_mapfiles/KEGG_pathways_info.tsv.gz
#add_descriptions.py -i KO_pathways_out/path_abun_unstrat.tsv.gz -o KEGG_pathways_out/path_abun_unstrat_descrip.tsv.gz --custom_map_table /home/jhuang/anaconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/description_mapfiles/KEGG_pathways_info.tsv.gz

#NOTE: Target-analysis for the pathway "mixed acid fermentation"

  4. Visualization

    #7.1 STAMP
#https://github.com/picrust/picrust2/wiki/STAMP-example
#Note that STAMP can only be opened under Windows

# It needs two files: path_abun_unstrat_descrip.tsv.gz as "Profile file" and metadata.tsv as "Group metadata file".
cp ~/DATA/Data_Karoline_16S_2025/picrust2_out_advanced/EC_pathways_out/path_abun_unstrat_descrip.tsv ~/DATA/Access_to_Win10/

cut -d$'\t' -f1 qiime2_metadata.tsv > 1
cut -d$'\t' -f3 qiime2_metadata.tsv > 3
cut -d$'\t' -f5-6 qiime2_metadata.tsv > 5_6
paste -d$'\t' 1 3 > 1_3
paste -d$'\t' 1_3 5_6 > metadata.tsv
#SampleID --> SampleID
SampleID        Group   pre_post        Sex_age
sample-A1       Group1  3d.post.stroke  male.aged
sample-A2       Group1  3d.post.stroke  male.aged
sample-A3       Group1  3d.post.stroke  male.aged
cp ~/DATA/Data_Karoline_16S_2025/metadata.tsv ~/DATA/Access_to_Win10/
# MANULLY_EDITING: keeping the only needed records in metadata.tsv: Group 9 (J1–J4, J10, J11) and Group 10 (K1–K6).

#7.2. ALDEx2
https://bioconductor.org/packages/release/bioc/html/ALDEx2.html

Under docker-env (qiime2-amplicon-2023.9)

  1. (NOT_NEEDED) Convert pathway output to BIOM and re-import to QIIME2 gunzip picrust2_out/pathways_out/path_abun_unstrat.tsv.gz biom convert \ -i picrust2_out/pathways_out/path_abun_unstrat.tsv \ -o picrust2_out/path_abun_unstrat.biom \ –table-type=”Pathway table” \ –to-hdf5

    qiime tools import \
--input-path picrust2_out/path_abun_unstrat.biom \
--type 'FeatureTable[Frequency]' \
--input-format BIOMV210Format \
--output-path path_abun.qza

#qiime tools export --input-path path_abun.qza --output-path exported_path_abun
#qiime tools peek path_abun.qza
echo "✅ PICRUSt2 pipeline complete. Output in: picrust2_out"

  2. Short answer: unless you had a very clear, pre-specified directional hypothesis, you should use a two-sided test.

    A bit more detail:

* Two-sided t-test

        * Tests: “Are the means different?” (could be higher or lower).
        * Standard default in most biological and clinical studies and usually what reviewers expect.
        * More conservative than a one-sided test.

* One-sided t-test

        * Tests: “Is Group A greater than Group B?” (or strictly less than).
        * You should only use it if before looking at the data you had a strong reason to expect a specific direction and you would ignore/consider uninterpretable a difference in the opposite direction.
        * Using one-sided just to gain significance is considered bad practice.

For your pathway analysis (exploratory, many pathways, q-value correction), the safest and most defensible choice is to:

* Use a two-sided t-test (equal variance or Welch’s, depending on variance assumptions).

So I’d recommend rerunning STAMP with Type: Two-sided and reporting those results.

#--> Using a two-sided Welch's t-test in STAMP, that is the unequal-variance version (does not assume equal variances and is more conservative than “t-test (equal variance)” referring to the classical unpaired Student’s t-test.

  3. Statistics in STAMP

    * For multiple groups:
    * Statistical test: ANOVA, Kruskal-Wallis H-test
    * Post-hoc test: Games-Howell, Scheffe, Tukey-Kramer, Welch's (uncorrected) (by default 0.95)
    * Effect size: Eta-squared
    * Multiple test correction: Benjamini-Hochberg FDR, Bonferroni, No correction
* For two groups
    * Statistical test: t-test (equal variance), Welch's t-test, White's non-parametric t-test
    * Type: One-sided, Two-sided
    * CI method: "DP: Welch's inverted" (by default 0.95)
    * Multiple test correction: Benjamini-Hochberg FDR, Bonferroni, No correction, Sidak, Storey FDR
* For two samples
    * Statistical test: Bootstrap, Chi-square test, Chi-square test (w/Yates'), Difference between proportions, Fisher's exact test, G-test, G-test (w/Yates'), G-test (w/Yates') + Fisher's, Hypergeometric, Permutation
    * Type: One-sided, Two-sided
    * CI method: "DP: Asymptotic", "DP: Asymptotic-CC", "DP: Newcomber-Wilson", "DR: Haldane adjustment", "RP: Asymptotic" (by default 0.95)
    * Multiple test correction: Benjamini-Hochberg FDR, Bonferroni, No correction, Sidak, Storey FDR

  4. Since MetaCyc does not have a single pathway explicitly named “short-chain fatty acid biosynthesis”, I defined a small SCFA-related set (acetate-, propionate- and butyrate-producing pathways) and tested these between Group 9 and Group 10 (Welch’s t-test, with BH correction within this subset). These pathways can also be found in the file Welchs_t-test.xlsx attached to my email from 26.11.2025 (for Group9 (J1-4, J6-7, J10-11) vs Group10 (K1-6)).

Pathway ID  Description     Group 9 mean (%)    Group 10 mean (%)   p-value     p-adj (BH, SCFA set)
P108-PWY    pyruvate fermentation to propanoate I   0.5070  0.3817  0.001178    0.0071
PWY-5100    pyruvate fermentation to acetate and lactate II     0.8354  0.9687  0.007596    0.0228
CENTFERM-PWY    pyruvate fermentation to butanoate  0.0766  0.0410  0.026608    0.0532
PWY-5677    succinate fermentation to butanoate     0.0065  0.0088  0.365051    0.5476
P163-PWY    L-lysine fermentation to acetate and butanoate  0.0324  0.0271  0.484704    0.5816
PWY-5676    acetyl-CoA fermentation to butanoate II     0.1397  0.1441  0.927588    0.9276

In this SCFA-focused set, the propionate (P108-PWY) and acetate (PWY-5100) pathways remain significantly different between Group 9 and Group 10 after adjustment, whereas the butyrate-related pathways do not show clear significant differences (CENTFERM-PWY is borderline).

from 14.01.2026 (for Group9 (J1-4, J10-11) vs Group10 (K1-6)), marked green in the Excel-files.

Pathway ID  Description Group 9 mean (%)    Group 10 mean (%)   p-value p-adj (BH, 6-pathway set)
P108-PWY    pyruvate fermentation to propanoate I   0.5142  0.3817  0.001354    0.008127
PWY-5100    pyruvate fermentation to acetate and lactate II 0.8401  0.9687  0.008763    0.026290
CENTFERM-PWY    pyruvate fermentation to butanoate  0.0729  0.0410  0.069958    0.139916
PWY-5677    succinate fermentation to butanoate 0.0063  0.0088  0.367586    0.551379
P163-PWY    L-lysine fermentation to acetate and butanoate  0.0308  0.0271  0.693841    0.832609
PWY-5676    acetyl-CoA fermentation to butanoate II 0.1421  0.1441  0.971290    0.971290

  1. Reporting

    Please find attached the results of the pathway analysis. The Excel file contains the full statistics for all pathways; those with adjusted p-values (Benjamini–Hochberg) ≤ 0.05 are highlighted in yellow and are the ones illustrated in the figure.

The analysis was performed using Welch’s t-test (two-sided) with Benjamini–Hochberg correction for multiple testing.

browse the 141 pipelines that are currently available as part of nf-core on 2026-01-14

Leave a reply

Count check

  • Input pipeline count: 141
  • Output pipeline count (below): 141 ✅
  • Categories: 16
  • Sum of category counts: 141 ✅

Categorized pipelines (with counts)

1) Bulk RNA-seq & transcriptomics (19)

alleleexpression, cageseq, circrna, denovotranscript, differentialabundance, drop, dualrnaseq, evexplorer, isoseq, lncpipe, nanostring, nascent, rnafusion, rnaseq, rnasplice, rnavar, riboseq, slamseq, stableexpression

2) Small RNA-seq (1)

smrnaseq

3) Single-cell transcriptomics (6)

marsseq, scdownstream, scflow, scnanoseq, scrnaseq, smartseq2

4) Spatial omics (6)

molkart, panoramaseq, pixelator, sopa, spatialvi, spatialxe

5) Chromatin & regulation (10)

atacseq, callingcards, chipseq, clipseq, cutandrun, hic, hicar, mnaseseq, sammyseq, tfactivity

6) DNA methylation (3)

methylarray, methylong, methylseq

7) Human genomics, variants & disease (22)

abotyper, circdna, deepvariant, eager, exoseq, gwas, longraredisease, mitodetect, oncoanalyser, pacvar, phaseimpute, radseq, raredisease, rarevariantburden, rnadnavar, sarek, ssds, tumourevo, variantbenchmarking, variantcatalogue, variantprioritization, createpanelrefs

8) Viruses & pathogen surveillance (7)

pathogensurveillance, phageannotator, tbanalyzer, viralmetagenome, viralintegration, viralrecon, vipr

9) Metagenomics & microbiome (10)

ampliseq, coproid, createtaxdb, detaxizer, funcscan, mag, magmap, metapep, metatdenovo, taxprofiler

10) Genome assembly, annotation & comparative genomics (14)

bacass, bactmap, denovohybrid, genomeannotator, genomeassembler, genomeqc, genomeskim, hgtseq, multiplesequencealign, neutronstar, pangenome, pairgenomealign, phyloplace, reportho

11) Immunology & antigen presentation (4)

airrflow, epitopeprediction, hlatyping, mhcquant

12) Proteomics, metabolomics & protein informatics (11)

ddamsproteomics, diaproteomics, kmermaid, metaboigniter, proteinannotator, proteinfamilies, proteinfold, proteogenomicsdb, proteomicslfq, quantms, ribomsqc

13) Imaging & other experimental modalities (7)

cellpainting, imcyto, liverctanalysis, lsmquant, mcmicro, rangeland, troughgraph

14) Data acquisition, QC & ops / utilities (12)

bamtofastq, datasync, demo, demultiplex, fastqrepair, fastquorum, fetchngs, nanoseq, readsimulator, references, seqinspector, seqsubmit

15) Genome editing & screens (2)

crisprseq, crisprvar

16) Other methods / modelling / non-bioinformatics (7)

deepmodeloptim, deepmutscan, diseasemodulediscovery, drugresponseeval, meerpipe, omicsgenetraitassociation, spinningjenny

Category Name Short description 中文描述 Released Stars Last release
Bulk RNA-seq & transcriptomics alleleexpression Allele-specific expression (ASE) analysis using STAR-WASP, UMI-tools, phaser 等位基因特异性表达（ASE）分析：STAR-WASP 比对，UMI-tools 去重，phaser 单倍型分相与 ASE 检测 2 –
Bulk RNA-seq & transcriptomics cageseq CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags. CAGE-seq 分析：剪切、比对并统计 CAGE 标签（转录起始相关）。 11 1.0.2
Bulk RNA-seq & transcriptomics circrna circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data 环状 RNA（circRNA）定量、差异表达分析及 miRNA 靶标预测。 59 –
Bulk RNA-seq & transcriptomics denovotranscript de novo transcriptome assembly of paired-end short reads from bulk RNA-seq 基于 bulk RNA-seq 双端短读长的从头转录组组装。 19 1.2.1
Bulk RNA-seq & transcriptomics differentialabundance Differential abundance analysis for feature/observation matrices (e.g., RNA-seq) 对特征/观测矩阵做差异丰度分析（可用于表达矩阵等）。 87 1.5.0
Bulk RNA-seq & transcriptomics drop Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders RNA-seq 异常事件检测流程（用于罕见病诊断等）。 7 –
Bulk RNA-seq & transcriptomics dualrnaseq Analysis of Dual RNA-seq data (host-pathogen interactions) 宿主-病原双 RNA-seq 分析流程，用于研究宿主-病原相互作用。 25 1.0.0
Bulk RNA-seq & transcriptomics evexplorer Analyze RNA data from extracellular vesicles; QC, region detection, normalization, DRE 胞外囊泡（EV）RNA 数据分析：质控、表达区域检测、归一化与差异 RNA 表达（DRE）。 1 –
Bulk RNA-seq & transcriptomics isoseq Genome annotation with PacBio Iso-Seq from raw subreads to FLNC and bed annotation PacBio Iso-Seq 基因组注释：从 subreads 生成 FLNC 并产出 bed 注释。 50 2.0.0
Bulk RNA-seq & transcriptomics lncpipe Analysis of long non-coding RNAs from RNA-seq datasets (under development) lncRNA（长链非编码 RNA）分析流程（开发中）。 34 –
Bulk RNA-seq & transcriptomics nanostring Analysis pipeline for Nanostring nCounter expression data. Nanostring nCounter 表达数据分析流程。 16 1.3.1
Bulk RNA-seq & transcriptomics nascent Nascent Transcription Processing Pipeline 新生转录（nascent RNA）处理与分析流程。 22 2.3.0
Bulk RNA-seq & transcriptomics rnafusion RNA-seq analysis pipeline for detection of gene-fusions RNA-seq 融合基因检测流程。 170 4.0.0
Bulk RNA-seq & transcriptomics rnaseq RNA sequencing pipeline (STAR/RSEM/HISAT2/Salmon) with QC and counts 常规 bulk RNA-seq 分析：比对/定量/计数与全面质控（多比对/定量器可选）。 1179 3.22.2
Bulk RNA-seq & transcriptomics rnasplice RNA-seq alternative splicing analysis RNA-seq 可变剪接分析流程。 63 1.0.4
Bulk RNA-seq & transcriptomics rnavar gatk4 RNA variant calling pipeline 基于 GATK4 的 RNA 变异检测（RNA variant calling）。 58 1.2.2
Bulk RNA-seq & transcriptomics riboseq Analysis of ribosome profiling (Ribo-seq) data Ribo-seq（核糖体测序/核糖体 footprinting）分析流程。 21 1.2.0
Bulk RNA-seq & transcriptomics slamseq SLAMSeq processing and analysis pipeline SLAM-seq（新生 RNA 标记）处理与分析流程。 10 1.0.0
Bulk RNA-seq & transcriptomics stableexpression Identify stable genes across datasets; useful for RT-qPCR reference genes 寻找最稳定基因（适合作为 RT-qPCR 参考内参基因）。 5 –
Small RNA-seq smrnaseq A small-RNA sequencing analysis pipeline 小 RNA 测序（如 miRNA 等）分析流程。 98 2.4.1
Single-cell transcriptomics marsseq MARS-seq v2 pre-processing pipeline with velocity MARS-seq v2 预处理流程，支持 RNA velocity。 8 1.0.3
Single-cell transcriptomics scdownstream Single cell transcriptomics pipeline for QC, integration, presentation 单细胞转录组下游：质控、整合与结果展示。 81 –
Single-cell transcriptomics scflow Please consider using/contributing to nf-core/scdownstream 单细胞流程（建议转向/贡献 scdownstream）。 25 –
Single-cell transcriptomics scnanoseq Single-cell/nuclei pipeline for Oxford Nanopore + 10x Genomics 单细胞/细胞核测序流程：结合 ONT 与 10x 数据。 52 1.2.1
Single-cell transcriptomics scrnaseq Single-cell RNA-Seq pipeline (10x/DropSeq/SmartSeq etc.) 单细胞 RNA-seq 主流程：支持 10x、DropSeq、SmartSeq 等。 310 4.1.0
Single-cell transcriptomics smartseq2 Process single cell RNA-seq generated with SmartSeq2 SmartSeq2 单细胞 RNA-seq 处理流程。 15 –
Spatial omics molkart Processing Molecular Cartography data (Resolve Bioscience combinatorial FISH) Resolve Molecular Cartography（组合 FISH）数据处理流程。 14 1.2.0
Spatial omics panoramaseq Pipeline to process sequencing-based spatial transcriptomics data (in-situ arrays) 测序型空间转录组（in-situ arrays）数据处理流程。 0 –
Spatial omics pixelator Pipeline to generate Molecular Pixelation data (Pixelgen) Pixelgen 分子像素化（Molecular Pixelation）数据处理流程。 13 2.3.0
Spatial omics sopa Nextflow version of Sopa – spatial omics pipeline and analysis Sopa 的 Nextflow 实现：空间组学流程与分析。 11 –
Spatial omics spatialvi Process spatial gene counts + spatial coordinates + image data (10x Visium) 10x Visium 空间转录组处理：基因计数+空间坐标+图像数据。 70 –
Spatial omics spatialxe (no description shown) 空间组学相关流程（原表未给出描述）。 24 –
Chromatin & regulation atacseq ATAC-seq peak-calling and QC analysis pipeline ATAC-seq 峰识别与质控分析流程。 221 2.1.2
Chromatin & regulation callingcards A pipeline for processing calling cards data Calling cards 实验数据处理流程。 6 1.0.0
Chromatin & regulation chipseq ChIP-seq peak-calling, QC and differential analysis ChIP-seq 峰识别、质控与差异分析流程。 229 2.1.0
Chromatin & regulation clipseq CLIP-seq QC, mapping, UMI deduplication, peak-calling options CLIP-seq 分析：质控、比对、UMI 去重与多种 peak calling。 24 1.0.0
Chromatin & regulation cutandrun CUT&RUN / CUT&TAG pipeline with QC, spike-ins, IgG controls, peak calling CUT&RUN/CUT&TAG 分析：质控、spike-in、IgG 对照、峰识别与下游。 106 3.2.2
Chromatin & regulation hic Analysis of Chromosome Conformation Capture (Hi-C) data Hi-C 染色体构象捕获数据分析流程。 105 2.1.0
Chromatin & regulation hicar HiCAR multi-omic co-assay pipeline HiCAR 多组学共测（转录+染色质可及性+接触）分析流程。 12 1.0.0
Chromatin & regulation mnaseseq MNase-seq analysis pipeline using BWA and DANPOS2 MNase-seq 分析流程（BWA + DANPOS2）。 12 1.0.0
Chromatin & regulation sammyseq SAMMY-seq pipeline to analyze chromatin state SAMMY-seq 染色质状态分析流程。 5 –
Chromatin & regulation tfactivity Identify differentially active TFs using expression + open chromatin 整合表达与开放染色质数据，识别差异活跃转录因子（TF）。 12 –
DNA methylation methylarray Illumina methylation array processing; QC, confounders, DMP/DMR, cell comp optional Illumina 甲基化芯片分析：预处理、质控、混杂因素检查、DMP/DMR；可选细胞组成估计与校正。 6 –
DNA methylation methylong Extract methylation calls from long reads (ONT/PacBio) 从长读长（ONT/PacBio）提取甲基化识别结果。 19 2.0.0
DNA methylation methylseq Bisulfite-seq methylation pipeline (Bismark/bwa-meth + MethylDackel/rastair) 亚硫酸氢盐测序甲基化分析流程（Bismark/bwa-meth 等）。 185 4.2.0
Human genomics, variants & disease abotyper Characterise human blood group and red cell antigens using ONT 基于 ONT 的人类血型与红细胞抗原分型/鉴定流程。 1 –
Human genomics, variants & disease circdna Identify extrachromosomal circular DNA (ecDNA) from Circle-seq/WGS/ATAC-seq 从 Circle-seq/WGS/ATAC-seq 识别染色体外环状 DNA（ecDNA）。 31 1.1.0
Human genomics, variants & disease createpanelrefs Generate Panel of Normals / models / references from many samples 从大量样本生成 PoN（Panel of Normals）/模型/参考资源。 11 –
Human genomics, variants & disease deepvariant Consider using/contributing to nf-core/sarek DeepVariant 相关（建议使用/贡献至 sarek）。 40 1.0
Human genomics, variants & disease eager Ancient DNA analysis pipeline 古 DNA（aDNA）分析流程（可重复、标准化）。 195 2.5.3
Human genomics, variants & disease exoseq Please consider using/contributing to nf-core/sarek Exo-seq 相关（建议使用/贡献至 sarek）。 16 –
Human genomics, variants & disease gwas UNDER CONSTRUCTION: Genome Wide Association Studies GWAS（全基因组关联分析）流程（建设中）。 27 –
Human genomics, variants & disease longraredisease Long-read sequencing pipeline for rare disease variant discovery 长读长测序罕见病变异识别流程（神经发育障碍等）。 5 v1.0.0-alpha
Human genomics, variants & disease mitodetect A-Z analysis of mitochondrial NGS data 线粒体 NGS 数据全流程分析。 7 –
Human genomics, variants & disease oncoanalyser Comprehensive cancer DNA/RNA analysis and reporting pipeline 肿瘤 DNA/RNA 综合分析与报告生成流程。 97 2.3.0
Human genomics, variants & disease pacvar Long-read PacBio sequencing processing for WGS and PureTarget PacBio 长读长 WGS/PureTarget 测序数据处理流程。 13 1.0.1
Human genomics, variants & disease phaseimpute Phase and impute genetic data 遗传数据分相与基因型填补流程。 27 1.1.0
Human genomics, variants & disease radseq Variant-calling pipeline for RADseq RADseq 变异检测流程。 7 –
Human genomics, variants & disease raredisease Call and score variants from WGS/WES of rare disease patients 罕见病 WGS/WES 变异检测与打分流程。 112 2.6.0
Human genomics, variants & disease rarevariantburden Summary count based rare variant burden test (e.g., vs gnomAD) 基于汇总计数的稀有变异负担检验（可与 gnomAD 等对照）。 0 –
Human genomics, variants & disease rnadnavar Integrated RNA+DNA somatic mutation detection RNA+DNA 联合分析的体细胞突变检测流程。 14 –
Human genomics, variants & disease sarek Germline/somatic variant calling + annotation from WGS/targeted WGS/靶向测序的生殖系/体细胞变异检测与注释（含预处理、calling、annotation）。 532 3.7.1
Human genomics, variants & disease ssds Single-stranded DNA Sequencing (SSDS) pipeline SSDS（单链 DNA 测序）分析流程。 1 –
Human genomics, variants & disease tumourevo Model tumour clonal evolution from WGS (CN, subclones, signatures) 基于 WGS 的肿瘤克隆进化建模（CN、亚克隆、突变签名等）。 20 –
Human genomics, variants & disease variantbenchmarking Evaluate/validate variant calling accuracy 变异检测方法准确性评估与验证流程（benchmark）。 37 1.4.0
Human genomics, variants & disease variantcatalogue Generate population variant catalogues from WGS 从 WGS 构建人群变异目录（变异列表及频率）。 13 –
Human genomics, variants & disease variantprioritization (no description shown) 变异优先级筛选流程（原表未给出描述）。 12 –
Viruses & pathogen surveillance pathogensurveillance Surveillance of pathogens using population genomics and sequencing 基于群体基因组与测序的病原体监测流程。 52 1.0.0
Viruses & pathogen surveillance phageannotator Identify, annotate, quantify phage sequences in (meta)genomes 在（宏）基因组中识别、注释并定量噬菌体序列。 17 –
Viruses & pathogen surveillance tbanalyzer Pipeline for Mycobacterium tuberculosis complex analysis 结核分枝杆菌复合群（MTBC）分析流程。 13 –
Viruses & pathogen surveillance viralmetagenome Untargeted viral genome reconstruction with iSNV detection from metagenomes 宏基因组中无靶向病毒全基因组重建，并检测 iSNV。 28 1.0.1
Viruses & pathogen surveillance viralintegration Identify viral integration events using chimeric reads 基于嵌合 reads 的病毒整合事件检测流程。 17 0.1.1
Viruses & pathogen surveillance viralrecon Viral assembly and intrahost/low-frequency variant calling 病毒组装与宿主体内/低频变异检测流程。 151 3.0.0
Viruses & pathogen surveillance vipr Viral assembly and intrahost/low-frequency variant calling 病毒组装与体内/低频变异检测流程（类似 viralrecon）。 14 –
Metagenomics & microbiome ampliseq Amplicon sequencing workflow using DADA2 and QIIME2 扩增子测序（如 16S/ITS）分析：DADA2 + QIIME2。 231 2.15.0
Metagenomics & microbiome coproid Coprolite host identification pipeline 粪化石（coprolite）宿主鉴定流程。 13 2.0.0
Metagenomics & microbiome createtaxdb Automated construction of classifier databases for multiple tools 自动化并行构建多种宏基因组分类工具的数据库。 20 2.0.0
Metagenomics & microbiome detaxizer Identify (and optionally remove) sequences; default remove human 识别并（可选）去除特定序列（默认去除人源污染）。 22 1.3.0
Metagenomics & microbiome funcscan (Meta-)genome screening for functional and natural product genes （宏）基因组功能基因与天然产物基因簇筛查。 99 3.0.0
Metagenomics & microbiome mag Assembly and binning of metagenomes 宏基因组组装与分箱（MAG 构建）。 264 5.3.0
Metagenomics & microbiome magmap Mapping reads to large collections of genomes 将 reads 比对到大型基因组集合的最佳实践流程。 10 1.0.0
Metagenomics & microbiome metapep From metagenomes to epitopes and beyond 从宏基因组到表位（epitope）等免疫相关下游分析。 12 1.0.0
Metagenomics & microbiome metatdenovo De novo assembly/annotation of metatranscriptomic or metagenomic data 宏转录组/宏基因组的从头组装与注释（支持原核/真核/病毒）。 34 1.3.0
Metagenomics & microbiome taxprofiler Multi-taxonomic profiling of shotgun short/long read metagenomics shotgun 宏基因组多类群（多生物界）分类谱分析（短读长/长读长）。 175 1.2.5
Genome assembly, annotation & comparative genomics bacass Simple bacterial assembly and annotation pipeline 简单的细菌组装与注释流程。 80 2.5.0
Genome assembly, annotation & comparative genomics bactmap Mapping-based pipeline for bacterial phylogeny from WGS 基于比对的细菌 WGS 系统发育/建树流程。 61 1.0.0
Genome assembly, annotation & comparative genomics denovohybrid Hybrid genome assembly pipeline (under construction) 混合组装流程（长+短读长）（建设中）。 8 –
Genome assembly, annotation & comparative genomics genomeannotator Identify (coding) gene structures in draft genomes 草图基因组（draft genome）基因结构（编码基因）注释流程。 34 –
Genome assembly, annotation & comparative genomics genomeassembler Assembly and scaffolding from long ONT/PacBio HiFi reads 长读长（ONT/PacBio HiFi）基因组组装与脚手架构建。 31 1.1.0
Genome assembly, annotation & comparative genomics genomeqc Compare quality of multiple genomes and annotations 比较多个基因组及其注释质量。 19 –
Genome assembly, annotation & comparative genomics genomeskim QC/filter genome skims; organelle assembly and/or analysis genome skim 数据质控/过滤，并进行细胞器组装或相关分析。 3 –
Genome assembly, annotation & comparative genomics hgtseq Investigate horizontal gene transfer from NGS data 从 NGS 数据研究水平基因转移（HGT）。 26 1.1.0
Genome assembly, annotation & comparative genomics multiplesequencealign Systematically evaluate MSA methods 多序列比对（MSA）方法系统评估流程。 40 1.1.1
Genome assembly, annotation & comparative genomics neutronstar De novo assembly for 10x linked-reads using Supernova 10x linked-reads 从头组装流程（Supernova）。 3 1.0.0
Genome assembly, annotation & comparative genomics pangenome Render sequences into a pangenome graph 将序列集合渲染为泛基因组图（pangenome graph）。 102 1.1.3
Genome assembly, annotation & comparative genomics pairgenomealign Pairwise genome comparison with LAST + plots 基于 LAST 的两两基因组比对与可视化绘图。 10 2.2.1
Genome assembly, annotation & comparative genomics phyloplace Phylogenetic placement with EPA-NG 使用 EPA-NG 的系统发育定位（placement）流程。 13 2.0.0
Genome assembly, annotation & comparative genomics reportho Comparative analysis of ortholog predictions 直系同源（ortholog）预测结果的比较分析流程。 11 1.1.0
Immunology & antigen presentation airrflow AIRR-seq repertoire analysis using Immcantation 免疫受体库（BCR/TCR，AIRR-seq）分析：基于 Immcantation。 73 4.3.1
Immunology & antigen presentation epitopeprediction Epitope prediction and annotation pipeline 表位（epitope）预测与注释流程。 50 3.1.0
Immunology & antigen presentation hlatyping Precision HLA typing from NGS data 基于 NGS 的高精度 HLA 分型流程。 76 2.1.0
Immunology & antigen presentation mhcquant Identify and quantify MHC eluted peptides from MS raw data 从质谱原始数据识别并定量 MHC 洗脱肽段。 42 3.1.0
Proteomics, metabolomics & protein informatics ddamsproteomics Quantitative shotgun MS proteomics 定量 shotgun 质谱蛋白组流程。 4 –
Proteomics, metabolomics & protein informatics diaproteomics Automated quantitative analysis of DIA proteomics MS measurements DIA 蛋白组质谱数据自动化定量分析流程。 21 1.2.4
Proteomics, metabolomics & protein informatics kmermaid k-mer similarity analysis pipeline k-mer 相似性分析流程。 23 0.1.0-alpha
Proteomics, metabolomics & protein informatics metaboigniter Metabolomics MS pre-processing with identification/quantification (MS1/MS2) 代谢组质谱预处理：基于 MS1/MS2 的鉴定与定量。 24 2.0.1
Proteomics, metabolomics & protein informatics proteinannotator Protein fasta → annotations 蛋白序列（FASTA）到注释的自动化流程。 8 –
Proteomics, metabolomics & protein informatics proteinfamilies Generation and updating of protein families 蛋白家族的生成与更新流程。 21 2.2.0
Proteomics, metabolomics & protein informatics proteinfold Protein 3D structure prediction pipeline 蛋白三维结构预测流程。 94 1.1.1
Proteomics, metabolomics & protein informatics proteogenomicsdb Generate protein databases for proteogenomics analysis 构建蛋白基因组学分析所需的蛋白数据库。 7 1.0.0
Proteomics, metabolomics & protein informatics proteomicslfq Proteomics label-free quantification (LFQ) analysis pipeline 蛋白组无标记定量（LFQ）分析流程。 37 1.0.0
Proteomics, metabolomics & protein informatics quantms Quantitative MS workflow (DDA-LFQ, DDA-Isobaric, DIA-LFQ) 定量蛋白组流程：支持 DDA-LFQ、等标记 DDA、DIA-LFQ 等。 34 1.2.0
Proteomics, metabolomics & protein informatics ribomsqc QC pipeline monitoring MS performance in ribonucleoside analysis 核苷相关质谱分析的性能监控与质控流程。 0 –
Imaging & other modalities cellpainting (no description shown) Cell Painting 相关流程（原表未给出描述）。 8 –
Imaging & other modalities imcyto Image Mass Cytometry analysis pipeline 成像质谱细胞术（IMC）图像/数据分析流程。 26 1.0.0
Imaging & other modalities liverctanalysis UNDER CONSTRUCTION: pipeline for liver CT analysis 肝脏 CT 影像分析流程（建设中）。 0 –
Imaging & other modalities lsmquant Process and analyze light-sheet microscopy images 光片显微（light-sheet）图像处理与分析流程。 5 –
Imaging & other modalities mcmicro Whole-slide multi-channel image processing to single-cell data 多通道全切片图像到单细胞数据的端到端处理流程。 29 –
Imaging & other modalities rangeland Remotely sensed imagery pipeline for land-cover trend files 遥感影像处理流程：结合辅助数据生成土地覆盖变化趋势文件。 9 1.0.0
Imaging & other modalities troughgraph Quantitative assessment of permafrost landscapes and thaw level 冻土景观与冻融程度的定量评估流程。 2 –
Data acquisition, QC & utilities bamtofastq Convert BAM/CRAM to FASTQ and perform QC BAM/CRAM 转 FASTQ 并进行质控。 31 2.2.0
Data acquisition, QC & utilities datasync System operation / automation workflows 系统运维/自动化工作流（数据同步与操作任务）。 10 –
Data acquisition, QC & utilities demo Simple nf-core style pipeline for workshops and demos nf-core 风格的示例/教学演示流程。 10 1.0.2
Data acquisition, QC & utilities demultiplex Demultiplexing pipeline for sequencing data 测序数据拆样/解复用流程。 52 1.7.0
Data acquisition, QC & utilities fastqrepair Recover corrupted FASTQ.gz, fix reads, remove unpaired, reorder 修复损坏 FASTQ.gz：修正不合规 reads、移除未配对 reads、重排序等。 6 1.0.0
Data acquisition, QC & utilities fastquorum Produce consensus reads using UMIs/barcodes 基于 UMI/条形码生成共识 reads 的流程。 27 1.2.0
Data acquisition, QC & utilities fetchngs Fetch metadata and raw FastQ files from public databases 从公共数据库抓取元数据与原始 FASTQ。 185 1.12.0
Data acquisition, QC & utilities nanoseq Nanopore demultiplexing, QC and alignment pipeline Nanopore 数据拆样、质控与比对流程。 218 3.1.0
Data acquisition, QC & utilities readsimulator Simulate sequencing reads (amplicon, metagenome, WGS, etc.) 测序 reads 模拟流程（扩增子、靶向捕获、宏基因组、全基因组等）。 33 1.0.1
Data acquisition, QC & utilities references Build references for multiple use cases 多用途参考资源构建流程。 19 0.1
Data acquisition, QC & utilities seqinspector QC-only pipeline producing global/group-specific MultiQC reports 纯质控流程：运行多种 QC 工具并输出全局/分组 MultiQC 报告。 16 –
Data acquisition, QC & utilities seqsubmit Submit data to ENA 向 ENA 提交数据的流程。 3 –
Genome editing & screens crisprseq CRISPR edited data analysis (targeted + screens) CRISPR 编辑数据分析：靶向编辑质量评估与 pooled screen 关键基因发现。 53 2.3.0
Genome editing & screens crisprvar Evaluate outcomes from genome editing experiments (WIP) 基因编辑实验结果评估流程（WIP）。 5 –
Other methods / modelling / non-bio deepmodeloptim Stochastic Testing and Input Manipulation for Unbiased Learning Systems 无偏学习系统的随机测试与输入操控（机器学习相关）。 28 –
Other methods / modelling / non-bio deepmutscan Deep mutational scanning (DMS) analysis pipeline 深度突变扫描（DMS）数据分析流程。 3 –
Other methods / modelling / non-bio diseasemodulediscovery Network-based disease module identification 基于网络的疾病模块识别流程。 5 –
Other methods / modelling / non-bio drugresponseeval Evaluate drug response prediction models 药物反应预测模型的评估流程（统计与生物学上更严谨）。 24 1.1.0
Other methods / modelling / non-bio meerpipe Astronomy pipeline for MeerKAT pulsar data MeerKAT 脉冲星数据天文处理流程（成像与计时分析）。 10 –
Other methods / modelling / non-bio omicsgenetraitassociation Multi-omics integration and trait association analysis pipeline 多组学整合并进行性状/表型关联分析的流程。 11 –
Other methods / modelling / non-bio spinningjenny Simulating the first industrial revolution using agent-based models 基于主体（Agent-based）模型模拟第一次工业革命的流程。 4 –

nf-core pipelines (selected)

Leave a reply
  1. nf-core/viralmetagenome is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
  2. nf-core/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples.
  3. nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples.
  4. nfcore/ampliseq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S.
  5. nf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes.
  6. nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data.
  7. nf-core/funcscan is a bioinformatics best-practice analysis pipeline for the screening of nucleotide sequences such as assembled contigs for functional genes.
  8. nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input reference genome set in a highly automated and parallelised manner.
  9. nf-core/detaxizer is a bioinformatics pipeline that checks for the presence of a specific taxon in (meta)genomic fastq files and to filter out this taxon or taxonomic subtree.

Phyloseq_Group9_10_11_pre-FMT.Rmd

Leave a reply

author: “” date: ‘r format(Sys.time(), "%d %m %Y")‘ header-includes:

  • \usepackage{color, fancyvrb} output: rmdformats::readthedown: highlight: kate number_sections : yes pdf_document: toc: yes toc_depth: 2 number_sections : yes


#install.packages(c("picante", "rmdformats"))
#mamba install -c conda-forge freetype libpng harfbuzz fribidi
#mamba install -c conda-forge r-systemfonts r-svglite r-kableExtra freetype fontconfig harfbuzz fribidi libpng
library(knitr)
library(rmdformats)
library(readxl)
library(dplyr)
library(kableExtra)
library(openxlsx)
library(DESeq2)
library(writexl)

options(max.print="75")
knitr::opts_chunk$set(fig.width=8,
                      fig.height=6,
                      eval=TRUE,
                      cache=TRUE,
                      echo=TRUE,
                      prompt=FALSE,
                      tidy=FALSE,
                      comment=NA,
                      message=FALSE,
                      warning=FALSE)
opts_knit$set(width=85)
#rmarkdown::render('Phyloseq_Group9_10_11_pre-FMT.Rmd',output_file='Phyloseq_Group9_10_11_pre-FMT.html')
# Phyloseq R library
#* Phyloseq web site : https://joey711.github.io/phyloseq/index.html
#* See in particular tutorials for
#    - importing data: https://joey711.github.io/phyloseq/import-data.html
#    - heat maps: https://joey711.github.io/phyloseq/plot_heatmap-examples.html

Data

Import raw data and assign sample key:

#extend qiime2_metadata_for_qza_to_phyloseq.tsv with Diet and Flora
#setwd("~/DATA/Data_Laura_16S_2/core_diversity_e4753")
#map_corrected <- read.csv("qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1)
#knitr::kable(map_corrected) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

Prerequisites to be installed

install.packages("dplyr")     # To manipulate dataframes
install.packages("readxl")    # To read Excel files into R
install.packages("ggplot2")   # for high quality graphics
install.packages("heatmaply")
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
#mamba install -c conda-forge r-ggplot2 r-vegan r-data.table
#BiocManager::install("microbiome")
#install.packages("ggpubr")
#install.packages("heatmaply")
library("readxl") # necessary to import the data from Excel file
library("ggplot2") # graphics
library("picante")
library("microbiome") # data analysis and visualisation
library("phyloseq") # also the basis of data object. Data analysis and visualisation
library("ggpubr") # publication quality figures, based on ggplot2
library("dplyr") # data handling, filter and reformat data frames
library("RColorBrewer") # nice color options
library("heatmaply")
library(vegan)
library(gplots)
#install.packages("openxlsx")
library(openxlsx)

Read the data and create phyloseq objects

Three tables are needed

  • OTU
  • Taxonomy
  • Samples

    library(tidyr)

    # For QIIME1
    #ps.ng.tax <- import_biom("./exported_table/feature-table.biom", "./exported-tree/tree.nwk")

    # For QIIME2
    #install.packages("remotes")
    #remotes::install_github("jbisanz/qiime2R")
    #"core_metrics_results/rarefied_table.qza", rarefying performed in the code, therefore import the raw table.
    library(qiime2R)
    ps_raw <- qza_to_phyloseq(
      features =  "table.qza",  #cp ../Data_Karoline_16S_2025/dada2_tests2/test_7_f240_r240/table.qza .
      tree = "rooted-tree.qza",  #cp ../Data_Karoline_16S_2025/rooted-tree.qza .
      metadata = "qiime2_metadata_for_qza_to_phyloseq.tsv"  #cp ../Data_Karoline_16S_2025/qiime2_metadata_for_qza_to_phyloseq.tsv .
    )
    # or
    #biom convert \
    #      -i ./exported_table/feature-table.biom \
    #      -o ./exported_table/feature-table-v1.biom \
    #      --to-json
    #ps_raw <- import_biom("./exported_table/feature-table-v1.biom", treefilename="./exported-tree/tree.nwk")

    sample <- read.csv("./qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1)
    SAM = sample_data(sample, errorIfNULL = T)

    #> setdiff(rownames(SAM), sample_names(ps_raw))
    #[1] "sample-L9" should be removed since the low reads

    ps_base <- merge_phyloseq(ps_raw, SAM)
    print(ps_base)

    taxonomy <- read.delim("taxonomy.tsv", sep="\t", header=TRUE)  #cp ../Data_Karoline_16S_2025/exported-taxonomy/taxonomy.tsv .
    #head(taxonomy)
    # Separate taxonomy string into separate ranks
    taxonomy_df <- taxonomy %>% separate(Taxon, into = c("Domain","Phylum","Class","Order","Family","Genus","Species"), sep = ";", fill = "right", extra = "drop")
    # Use Feature.ID as rownames
    rownames(taxonomy_df) <- taxonomy_df$Feature.ID
    taxonomy_df <- taxonomy_df[, -c(1, ncol(taxonomy_df))]  # Drop Feature.ID and Confidence
    # Create tax_table
    tax_table_final <- phyloseq::tax_table(as.matrix(taxonomy_df))
    # Merge tax_table with existing phyloseq object
    ps_base <- merge_phyloseq(ps_base, tax_table_final)
    # Check
    ps_base

    #colnames(phyloseq::tax_table(ps_base)) <- c("Domain","Phylum","Class","Order","Family","Genus","Species")
    saveRDS(ps_base, "./ps_base.rds")

Visualize data

  sample_names(ps_base)
  rank_names(ps_base)
  sample_variables(ps_base)

  # Define sample names once
  samples <- c(
    #"sample-A1","sample-A2","sample-A5","sample-A6","sample-A7","sample-A8","sample-A9","sample-A10",  #RESIZED: "sample-A3","sample-A4","sample-A11",
    #"sample-B1","sample-B2","sample-B3","sample-B4","sample-B5","sample-B6","sample-B7",  #RESIZED: "sample-B8","sample-B9","sample-B10","sample-B11","sample-B12","sample-B13","sample-B14","sample-B15","sample-B16",
    #"sample-C1","sample-C2","sample-C3","sample-C4","sample-C5","sample-C6","sample-C7",  #RESIZED: "sample-C8","sample-C9","sample-C10",
    #"sample-E1","sample-E2","sample-E3","sample-E4","sample-E5","sample-E6","sample-E7","sample-E8","sample-E9","sample-E10",  #RESIZED:
    #"sample-F1","sample-F2","sample-F3","sample-F4","sample-F5",
    "sample-G1","sample-G2","sample-G3","sample-G4","sample-G5","sample-G6",
    "sample-H1","sample-H2","sample-H3","sample-H4","sample-H5","sample-H6",
    "sample-I1","sample-I2","sample-I3","sample-I4","sample-I5","sample-I6",
    "sample-J1","sample-J2","sample-J3","sample-J4","sample-J10","sample-J11",  #RESIZED: "sample-J5","sample-J8","sample-J9",     "sample-J6","sample-J7",
    "sample-K1","sample-K2","sample-K3","sample-K4","sample-K5","sample-K6",  #RESIZED: "sample-K7","sample-K8","sample-K9","sample-K10",    "sample-K11","sample-K12","sample-K13","sample-K14","sample-K15",
    "sample-L2","sample-L3","sample-L4","sample-L5","sample-L6"  #RESIZED:"sample-L1","sample-L7","sample-L8","sample-L10","sample-L11","sample-L12","sample-L13","sample-L14","sample-L15",
    #"sample-M1","sample-M2","sample-M3","sample-M4","sample-M5","sample-M6","sample-M7","sample-M8",
    #"sample-N1","sample-N2","sample-N3","sample-N4","sample-N5","sample-N6","sample-N7","sample-N8","sample-N9","sample-N10",
    #"sample-O1","sample-O2","sample-O3","sample-O4","sample-O5","sample-O6","sample-O7","sample-O8"
  )
  ps_pruned <- prune_samples(samples, ps_base)

  sample_names(ps_pruned)
  rank_names(ps_pruned)
  sample_variables(ps_pruned)

No samples were excluded as low-depth outliers (library sizes below the minimum depth threshold of 1,000 reads), and the remaining dataset (ps_filt) contains only samples meeting this depth cutoff with taxa retained only if they have nonzero total counts.

# ------------------------------------------------------------
#   Filter low-depth samples (recommended for all analyses)
# ------------------------------------------------------------
min_depth <- 1000  # <-- adjust to your data / study design, keeps all!
ps_filt <- prune_samples(sample_sums(ps_pruned) >= min_depth, ps_pruned)
ps_filt <- prune_taxa(taxa_sums(ps_filt) > 0, ps_filt)

# Keep a depth summary for reporting / QC
depth_summary <- summary(sample_sums(ps_filt))
depth_summary

Differential abundance (DESeq2) → ps_deseq: non-rarefied integer counts derived from ps_filt, with optional count-based taxon prefilter (default: taxa total counts ≥ 10 across all samples)

From ps_filt (e.g. 5669 taxa and 239 samples), we branch into analysis-ready objects in two directions:

  • Direction 1 for diversity analyses

    • Alpha diversity: ps_rarefied ✅ (common)
    • Beta diversity:
    • Unweighted UniFrac / Jaccard: ps_rarefied ✅ (often recommended)
    • Bray–Curtis / ordination on abundances: ps_rel or Hellinger ✅ (rarefaction optional)
    • Aitchison (CLR): CLR-transformed (non-rarefied) ✅ (no rarefaction)

Normalize number of reads in each sample using median sequencing depth.


# RAREFACTION
set.seed(9242)  # This will help in reproducing the filtering and nomalisation.
ps_rarefied <- rarefy_even_depth(ps_filt, sample.size = 6389)
#total <- 6389

# # NORMALIZE number of reads in each sample using median sequencing depth.
# total = median(sample_sums(ps.ng.tax))
# #> total
# #[1] 42369
# standf = function(x, t=total) round(t * (x / sum(x)))
# ps.ng.tax = transform_sample_counts(ps.ng.tax, standf)
# ps_rel <- microbiome::transform(ps.ng.tax, "compositional")
#
# saveRDS(ps.ng.tax, "./ps.ng.tax.rds")

  • Direction 2 for taxonomic composition plots

    • Taxonomic composition → ps_rel: relative abundance (compositional) computed after sample filtering (e.g. 5669 taxa and 239 samples)
    • Optional cleaner composition plots → ps_abund / ps_abund_rel: taxa filtered for plotting (e.g., keep taxa with mean relative abundance > 0.1%); (e.g. 95 taxa and 239 samples) ps_abund = counts, ps_abund_rel = relative abundance (use for visualization, not DESeq2)

For the heatmaps, we focus on the most abundant OTUs by first converting counts to relative abundances within each sample. We then filter to retain only OTUs whose mean relative abundance across all samples exceeds 0.1% (0.001). We are left with 199 OTUs which makes the reading much more easy.

# 1) Convert to relative abundances
ps_rel <- transform_sample_counts(ps_filt, function(x) x / sum(x))

# 2) Get the logical vector of which OTUs to keep (based on relative abundance)
keep_vector <- phyloseq::filter_taxa(
  ps_rel,
  function(x) mean(x) > 0.001,
  prune = FALSE
)

# 3) Use the TRUE/FALSE vector to subset absolute abundance data
ps_abund <- prune_taxa(names(keep_vector)[keep_vector], ps_filt)

# 4) Normalize the final subset to relative abundances per sample
ps_abund_rel <- transform_sample_counts(
  ps_abund,
  function(x) x / sum(x)
)
  library(stringr)
#for id in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100  101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206; do
#for id in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62; do
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"], \"__\")[[1]][2]"
#done
phyloseq::tax_table(ps_abund_rel)[1,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Species"], "__")[[1]][2]

Taxonomic summary

Bar plots in phylum level


  #aes(color="Phylum", fill="Phylum") --> aes()
  #ggplot(data=data, aes(x=Sample, y=Abundance, fill=Phylum))
  #options(max.print = 1e6)
  my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
  plot_bar(ps_abund_rel, fill="Phylum") + geom_bar(aes(), stat="identity", position="stack") +
  scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=2))                                  #6 instead of theme.size

\pagebreak Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

  ps_abund_rel_group <- merge_samples(ps_abund_rel, "G9_10_11_preFMT")
  #PENDING: The effect weighted twice by sum(x), is the same to the effect weighted once directly from absolute abundance?!
  ps_abund_rel_group_ = transform_sample_counts(ps_abund_rel_group, function(x) x / sum(x))
  #plot_bar(ps_abund_relSampleType_, fill = "Phylum") + geom_bar(aes(color=Phylum, fill=Phylum), stat="identity", position="stack")

  plot_bar(ps_abund_rel_group_, fill="Phylum") +
  geom_bar(stat="identity", position="stack") +
  scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
  scale_fill_manual(values = my_colors) +
  theme(
    axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
    axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
    axis.title.x = element_text(size = 12, colour = "black"),
    axis.title.y = element_text(size = 12, colour = "black")
  )

Bar plots in class level

  my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
  plot_bar(ps_abund_rel, fill="Class") + geom_bar(aes(), stat="identity", position="stack") +
  scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=3))

Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

  plot_bar(ps_abund_rel_group_, fill="Class") +
  geom_bar(stat="identity", position="stack") +
  scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
  scale_fill_manual(values = my_colors) +
  theme(
    axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
    axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
    axis.title.x = element_text(size = 12, colour = "black"),
    axis.title.y = element_text(size = 12, colour = "black")
  )

\pagebreak

Bar plots in order level

  my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
  plot_bar(ps_abund_rel, fill="Order") + geom_bar(aes(), stat="identity", position="stack") +
  scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=4))

Regroup together pre vs post stroke and normalize number of reads in each group using median sequencing depth.

  plot_bar(ps_abund_rel_group_, fill="Order") +
  geom_bar(stat="identity", position="stack") +
  scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
  scale_fill_manual(values = my_colors) +
  theme(
    axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
    axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
    axis.title.x = element_text(size = 12, colour = "black"),
    axis.title.y = element_text(size = 12, colour = "black")
  )

\pagebreak

Bar plots in family level

  my_colors <- c(
          "#FF0000", "#000000", "#0000FF", "#C0C0C0", "#FFFFFF", "#FFFF00", "#00FFFF", "#FFA500", "#00FF00", "#808080", "#FF00FF", "#800080", "#FDD017", "#0000A0", "#3BB9FF", "#008000", "#800000", "#ADD8E6", "#F778A1", "#800517", "#736F6E", "#F52887", "#C11B17", "#5CB3FF", "#A52A2A", "#FF8040", "#2B60DE", "#736AFF", "#1589FF", "#98AFC7", "#8D38C9", "#307D7E", "#F6358A", "#151B54", "#6D7B8D", "#FDEEF4", "#FF0080", "#F88017", "#2554C7", "#FFF8C6", "#D4A017", "#306EFF", "#151B8D", "#9E7BFF", "#EAC117", "#E0FFFF", "#15317E", "#6C2DC7", "#FBB917", "#FCDFFF", "#15317E", "#254117", "#FAAFBE", "#357EC7"
        )
  plot_bar(ps_abund_rel, fill="Family") + geom_bar(aes(), stat="identity", position="stack") +
  scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=8))

Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

  plot_bar(ps_abund_rel_group_, fill="Family") +
  geom_bar(stat="identity", position="stack") +
  scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
  scale_fill_manual(values = my_colors) +
  theme(
    axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
    axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
    axis.title.x = element_text(size = 12, colour = "black"),
    axis.title.y = element_text(size = 12, colour = "black")
  )

\pagebreak

\pagebreak

Alpha diversity

Plot Chao1 richness estimator, Observed OTUs, Shannon index, and Phylogenetic diversity. Regroup together samples from the same group.

# using rarefied data
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even42369.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_stool/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_swab/rep_set.tre

library(dplyr)
library(reshape2)
library(ggpubr)
library(phyloseq)
library(kableExtra)

# ------------------------------------------------------------
# 0) Restrict analysis to the specified sample subset
# ------------------------------------------------------------
stopifnot(exists("samples"))
stopifnot(exists("ps_rarefied"))

ps_rarefied_sub <- prune_samples(samples, ps_rarefied)

hmp.meta <- meta(ps_rarefied_sub)
hmp.meta$sam_name <- rownames(hmp.meta)

# ------------------------------------------------------------
# 1) Read QIIME2 alpha-diversity outputs
# ------------------------------------------------------------
shannon  <- read.table("exported_alpha/shannon/alpha-diversity.tsv",
                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)
faith_pd <- read.table("exported_alpha/faith_pd/alpha-diversity.tsv",
                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)
observed <- read.table("exported_alpha/observed_features/alpha-diversity.tsv",
                       header = TRUE, sep = "\t", stringsAsFactors = FALSE)

colnames(shannon)  <- c("sam_name", "shannon")
colnames(faith_pd) <- c("sam_name", "PD_whole_tree")
colnames(observed) <- c("sam_name", "observed_otus")

div.df <- Reduce(function(x, y) merge(x, y, by = "sam_name", all = FALSE),
                 list(shannon, faith_pd, observed))

# ------------------------------------------------------------
# 2) Merge in metadata (from the pruned phyloseq object)
# ------------------------------------------------------------
div.df <- merge(div.df, hmp.meta, by = "sam_name", all.x = TRUE, all.y = FALSE)

# Keep ONLY samples from the predefined list (safety net)
div.df <- div.df %>% filter(sam_name %in% samples)

# ------------------------------------------------------------
# 3) Collapse groups: Group6/7/8 -> pre-FMT; keep only 4 groups
# ------------------------------------------------------------
div.df <- div.df %>%
  mutate(
    Group4 = case_when(
      Group %in% c("Group6","Group7","Group8") ~ "pre-FMT",
      Group %in% c("Group9","Group10","Group11") ~ as.character(Group),
      TRUE ~ NA_character_
    ),
    Group4 = factor(Group4, levels = c("pre-FMT","Group9","Group10","Group11"))
  ) %>%
  filter(!is.na(Group4))

# ------------------------------------------------------------
# 4) Reformat table for reporting
# ------------------------------------------------------------
div.df2 <- div.df[, c("sam_name", "Group4", "shannon", "observed_otus", "PD_whole_tree")]
colnames(div.df2) <- c("Sample name", "Group", "Shannon", "OTU", "Phylogenetic Diversity")

write.csv(div.df2, file = "alpha_diversities_G9_10_11_preFMT.csv", row.names = FALSE)

#knitr::kable(div.df2) %>%
#  kable_styling(bootstrap_options = c("striped","hover","condensed","responsive"))

# ------------------------------------------------------------
# 5) QC: print which samples were used
# ------------------------------------------------------------
requested_samples <- samples
present_in_ps <- sample_names(ps_rarefied)

missing_in_ps <- setdiff(requested_samples, present_in_ps)

cat("\n==== QC: Sample selection (ps_rarefied) ====\n")
cat("Requested samples:", length(requested_samples), "\n")
cat("Present in ps_rarefied:", length(present_in_ps), "\n")
cat("Missing from ps_rarefied:", length(missing_in_ps), "\n")
if (length(missing_in_ps) > 0) print(missing_in_ps)

used_samples <- div.df2$`Sample name`
missing_in_alpha <- setdiff(requested_samples, used_samples)
extra_in_alpha <- setdiff(used_samples, requested_samples)

cat("\n==== QC: Samples used in alpha-div df (div.df2) ====\n")
cat("Used samples:", length(used_samples), "\n")
cat("Requested but NOT used:", length(missing_in_alpha), "\n")
if (length(missing_in_alpha) > 0) print(missing_in_alpha)
cat("Used but NOT requested (should be 0):", length(extra_in_alpha), "\n")
if (length(extra_in_alpha) > 0) print(extra_in_alpha)

qc_table <- div.df %>%
  select(sam_name, Group, Group4) %>%
  distinct() %>%
  arrange(Group4, Group, sam_name)

#cat("\n==== QC: Sample -> Group mapping used for plotting ====\n")
#print(qc_table)
#
#cat("\n==== QC: Counts per collapsed group (Group4) ====\n")
#print(div.df$Group4)

# ------------------------------------------------------------
# 6) Melt + plot
# ------------------------------------------------------------
div_df_melt <- reshape2::melt(
  div.df2,
  id.vars = c("Sample name","Group"),
  variable.name = "variable",
  value.name = "value"
)

# ensure final group order
div_df_melt$Group <- factor(div_df_melt$Group, levels = c("pre-FMT","Group9","Group10","Group11"))

#p <- ggboxplot(div_df_melt, x = "Group", y = "value",
#               facet.by = "variable",
#               scales = "free",
#               width = 0.5,
#               fill = "gray", legend = "right") +
#  theme(
#    axis.text.x  = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
#    axis.text.y  = element_text(size = 10),
#    axis.title.x = element_text(size = 12),
#    axis.title.y = element_text(size = 12)
#  )
# all pairwise comparisons among the 4 groups
#lev <- levels(droplevels(div_df_melt$Group))
#L.pairs <- combn(lev, 2, simplify = FALSE)
#
#p2 <- p + stat_compare_means(
#  method = "wilcox.test",
#  comparisons = L.pairs,
#  label = "p.signif",
#  p.adjust.method = "BH",
#  hide.ns = FALSE,
#  symnum.args = list(
#    cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1),
#    symbols   = c("****", "***", "**", "*", "ns")
#  )
#)
#p2

# ------------------------------------------------------------
# 7) Save figure
# ------------------------------------------------------------
#ggsave("./figures/alpha_diversity_G9_10_11_preFMT.png", p2, device="png", height = 10, width = 15, dpi = 300)
#ggsave("./figures/alpha_diversity_G9_10_11_preFMT.svg", p2, device="svg", height = 10, width = 15)

# ------------------------------------------------------------
# 8) Save statistics
# ------------------------------------------------------------

library(dplyr)
library(purrr)

# same pair list as in the plot
lev <- levels(droplevels(div_df_melt$Group))
L.pairs <- combn(lev, 2, simplify = FALSE)

# Pairwise Wilcoxon per metric, with BH adjustment (matches p.adjust.method="BH")
stats_for_plot <- div_df_melt %>%
  group_by(variable) %>%
  group_modify(~{
    dat <- .x

    res <- purrr::map_dfr(L.pairs, function(pr) {
      g1 <- pr[1]; g2 <- pr[2]
      x1 <- dat$value[dat$Group == g1]
      x2 <- dat$value[dat$Group == g2]

      wt <- suppressWarnings(wilcox.test(x1, x2, exact = FALSE))

      tibble(
        group1 = g1,
        group2 = g2,
        n1 = length(x1),
        n2 = length(x2),
        p = unname(wt$p.value)
      )
    })

    res %>%
      mutate(
        p.adj = p.adjust(p, method = "BH"),
        p.signif = case_when(
          p.adj <= 0.0001 ~ "****",
          p.adj <= 0.001  ~ "***",
          p.adj <= 0.01   ~ "**",
          p.adj <= 0.05   ~ "*",
          TRUE            ~ "ns"
        )
      )
  }) %>%
  ungroup() %>%
  rename(Metric = variable) %>%
  arrange(Metric, group1, group2)

# Print the exact statistics used for annotation
print(stats_for_plot, n = Inf)

write.csv(stats_for_plot, "./figures/alpha_diversity_pairwise_stats_used_for_plot.csv", row.names = FALSE)

library(openxlsx)

# (optional) make sure the folder exists
dir.create("./figures", showWarnings = FALSE, recursive = TRUE)

out_xlsx <- "./figures/alpha_diversity_pairwise_stats_used_for_plot.xlsx"

write.xlsx(
  x = list("pairwise_stats" = stats_for_plot),
  file = out_xlsx,
  overwrite = TRUE
)

cat("Saved Excel file to: ", out_xlsx, "\n", sep = "")
# ---------------------------------------------------------------------------------
# ----------------------------- draw plots from input -----------------------------

library(dplyr)
library(ggpubr)
library(reshape2)

# Example: read from a CSV file you wrote earlier
# stats_for_plot <- read.csv("./figures/alpha_diversity_pairwise_stats_used_for_plot.csv", stringsAsFactors = FALSE)

# Or if you paste as text:
txt <- 'Metric,group1,group2,n1,n2,p,p.adj,p.signif
Shannon,Group10,Group11,6,5,1,1,ns
Shannon,Group9,Group10,6,6,0.297953061608168,0.595906123216336,ns
Shannon,Group9,Group11,6,5,0.522816653919089,0.631819188094748,ns
Shannon,pre-FMT,Group10,18,6,0.017949090591566,0.0538472717746981,ns
Shannon,pre-FMT,Group11,18,5,0.00651735384842052,0.0391041230905231,*
Shannon,pre-FMT,Group9,18,6,0.526515990078957,0.631819188094748,ns
OTU,Group10,Group11,6,5,0.143214612017615,0.214821918026422,ns
OTU,Group9,Group10,6,6,0.229766270461138,0.275719524553366,ns
OTU,Group9,Group11,6,5,0.522816653919089,0.522816653919089,ns
OTU,pre-FMT,Group10,18,6,0.0015274145728676,0.00916448743720559,**
OTU,pre-FMT,Group11,18,5,0.0675601586409843,0.135120317281969,ns
OTU,pre-FMT,Group9,18,6,0.00759484512604444,0.0227845353781333,*
Phylogenetic Diversity,Group10,Group11,6,5,1,1,ns
Phylogenetic Diversity,Group9,Group10,6,6,1,1,ns
Phylogenetic Diversity,Group9,Group11,6,5,0.927264473525232,1,ns
Phylogenetic Diversity,pre-FMT,Group10,18,6,0.000361550896811121,0.00108465269043336,**
Phylogenetic Diversity,pre-FMT,Group11,18,5,0.000910436385913111,0.00182087277182622,**
Phylogenetic Diversity,pre-FMT,Group9,18,6,0.000361550896811121,0.00108465269043336,**'

stats_for_plot <- read.csv(textConnection(txt), stringsAsFactors = FALSE)

# Match naming to your plot data: your facet variable is called "variable"
stats_for_plot <- stats_for_plot %>%
  rename(variable = Metric) %>%
  mutate(
    group1 = factor(group1, levels = c("pre-FMT","Group9","Group10","Group11")),
    group2 = factor(group2, levels = c("pre-FMT","Group9","Group10","Group11"))
  )

# ------------------------------------------------------------
# Melt + plot (same as yours)
# ------------------------------------------------------------
div_df_melt <- reshape2::melt(
  div.df2,
  id.vars = c("Sample name","Group"),
  variable.name = "variable",
  value.name = "value"
)

div_df_melt$Group <- factor(div_df_melt$Group, levels = c("pre-FMT","Group9","Group10","Group11"))

p <- ggboxplot(div_df_melt, x = "Group", y = "value",
               facet.by = "variable",
               scales = "free",
               width = 0.5,
               fill = "gray", legend = "right") +
  theme(
    axis.text.x  = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
    axis.text.y  = element_text(size = 10),
    axis.title.x = element_text(size = 12),
    axis.title.y = element_text(size = 12)
  )

# ------------------------------------------------------------
# Add significance from your table (NO recomputation)
# ------------------------------------------------------------

# Compute y positions per facet so brackets don't overlap
ymax_by_metric <- div_df_melt %>%
  group_by(variable) %>%
  summarise(ymax = max(value, na.rm = TRUE), .groups = "drop")

stats_for_plot2 <- stats_for_plot %>%
  left_join(ymax_by_metric, by = "variable") %>%
  group_by(variable) %>%
  arrange(p.adj) %>%
  mutate(
    # stack brackets within each facet
    y.position = ymax * (1.05 + 0.08 * (row_number() - 1)),
    # what to display (stars or "ns")
    label = p.signif
  ) %>%
  ungroup()

p2 <- p +
  stat_pvalue_manual(
    stats_for_plot2,
    label = "label",
    xmin = "group1",
    xmax = "group2",
    y.position = "y.position",
    tip.length = 0.01,
    hide.ns = FALSE
  )

p2

# ------------------------------------------------------------
# Save
# ------------------------------------------------------------
ggsave("./figures/alpha_diversity_G9_10_11_preFMT_from_table.png",
       p2, device="png", height = 6, width = 9, dpi = 300)
ggsave("./figures/alpha_diversity_G9_10_11_preFMT_from_table.svg",
       p2, device="svg", height = 6, width = 9)
# label = sprintf("BH p=%.3g", p.adj)

Beta-diversity

Pairwise PERMANOVA tests

Pairwise PERMANOVA tests were performed on Bray–Curtis distance matrices to compare bacterial community composition between all pairs of sample groups (metadata column Group). For each pairwise comparison, the distance matrix was subset to samples from the two groups only, and significance was assessed using vegan::adonis2 with 9,999 permutations. Resulting p-values were adjusted for multiple testing using both Benjamini–Hochberg (BH/FDR) and Bonferroni corrections.

Bray_pairwise_PERMANOVA <- read.csv("figures_MP_Group9_10_11_PreFMT/Bray_pairwise_PERMANOVA.csv", sep = ",")
knitr::kable(Bray_pairwise_PERMANOVA, caption = "Pairwise PERMANOVA results (distance-based community differences among Group levels).") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

Global PERMANOVA on the weighted UniFrac distance matrix

Groups 9, 10, 11 vs the mixed pre-FMT group

# --- Global beta-diversity (PERMANOVA) ---
cat("```text\n")
cat(
"[PERMANOVA result]\n",
"The object contained internal attribute: PCoA ADONIS\n",
"Permutation test for adonis under reduced model\n",
"Permutation: free\n",
"Number of permutations: 9999\n",
"\n",
"vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)\n",
"         Df SumOfSqs      R2      F Pr(>F)    \n",
"Model     3   5.3256 0.58559 14.602  1e-04 ***\n",
"Residual 31   3.7689 0.41441                  \n",
"Total    34   9.0945 1.00000                  \n",
"---\n",
"Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1\n",
sep = ""
)
cat("```\n")

Groups 9, 10, 11

# --- Global beta-diversity (PERMANOVA) ---
cat("```text\n")
cat(
"[PERMANOVA result]\n",
"The object contained internal attribute: PCoA ADONIS\n",
"Permutation test for adonis under reduced model\n",
"Permutation: free\n",
"Number of permutations: 9999\n",
"\n",
"vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)\n",
"         Df SumOfSqs     R2      F Pr(>F)    \n",
"Model     2  0.82208 0.3324 3.4853  1e-04 ***\n",
"Residual 14  1.65109 0.6676                  \n",
"Total    16  2.47317 1.0000                  \n",
"---\n",
"Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1\n",
sep = ""
)
cat("```\n")

Principal coordinates analysis (PCoA) based on Bray–Curtis dissimilarity

Groups 9, 10, 11 vs the mixed pre-FMT group

knitr::include_graphics("figures_MP_Group9_10_11_PreFMT/PCoA3.png")

Groups 9, 10, 11

knitr::include_graphics("figures_MP_Group9_10_11/PCoA3.png")

Differential abundance analysis

Differential abundance analysis aims to find the differences in the abundance of each taxa between two groups of samples, assigning a significance value to each comparison.

Group 9 vs Group 10


# ------------------------------------------------------------
#  DESeq2: non-rarefied integer counts + optional taxon prefilter
# ------------------------------------------------------------
ps_deseq <- ps_filt

ps_deseq_sel2 <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel2) <- otu_table(ps_deseq)[,c("sample-J1","sample-J2","sample-J3","sample-J4","sample-J10","sample-J11",  "sample-K1","sample-K2","sample-K3","sample-K4","sample-K5","sample-K6")]
diagdds = phyloseq_to_deseq2(ps_deseq_sel2, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group9")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel2)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group9_vs_Group10"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
    scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
  theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
  geom_point(aes(size = padj)) +
  scale_size_continuous(name = "padj", range = c(8, 4)) +
  theme_bw() +
  theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics("DEGs_Group9_vs_Group10.png")

Microbiome analysis for Data_Karoline_16S_2025_cagefilter

Leave a reply

Microbiome analysis

Sample collection and storage

Fecal samples were collected from mice between 9–10 am at the indicated timepoints and immediately frozen at −80 °C until use. DNA extraction

Genomic DNA was extracted from fecal pellets using the QIAamp Fast DNA Stool Mini Kit (Qiagen, #51604) following a protocol optimized for murine stool. Briefly, pellets were mechanically homogenized in a Precellys® 24 homogenizer (Bertin Technologies) using Soil grinding tubes (Bertin Technologies, #SK38), and DNA was extracted according to the manufacturer’s instructions. DNA yield was measured with NanoDrop, and the concentration was adjusted to 10 ng/µl. 16S rRNA gene amplicon library preparation and sequencing

16S rRNA amplicons (V3–V4 region) were generated using degenerate primers that contain Illumina adapter overhang sequences: forward (5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3′) and reverse (5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC-3′), following established Illumina 16S library preparation guidance. [1] Samples were multiplexed using the Nextera XT Index Kit (Illumina, #FC-131-1001) and sequenced by 500-cycle paired-end sequencing (2×250 bp) on an Illumina MiSeq (Illumina, #MS-102-2003). Bioinformatics processing and QC

Raw FASTQ files were inspected with FastQC. [2] Sequence processing was performed in QIIME 2. [3] Demultiplexed paired-end reads were imported using a Phred33 manifest and per-base quality profiles were reviewed to guide trimming/truncation. ASVs were inferred using the QIIME 2 DADA2 workflow. [4] Primer/adapter-proximal bases were removed using fixed 5′ trimming (17 bp forward; 21 bp reverse), reads were filtered using expected-error thresholds, and multiple forward/reverse truncation length combinations were evaluated to optimize read retention and paired-end merging for the ~460 bp V3–V4 amplicon. Final denoising parameters were selected based on denoising statistics (successful merging and proportion of non-chimeric reads across samples), and the resulting feature table and representative ASV sequences were used for downstream analyses.

Taxonomy was assigned by VSEARCH-based consensus classification [5] against SILVA (release 132) [6] at 97% identity. Downstream visualization and statistics were performed in R using phyloseq. [7] Diversity analyses, ordination, and statistics

Alpha diversity (Observed features/OTU richness, Shannon diversity, and Faith’s phylogenetic diversity) was calculated on rarefied data and compared between groups using nonparametric rank-based tests (Wilcoxon rank-sum for two-group comparisons; Kruskal–Wallis for ≥3 groups with post-hoc pairwise Wilcoxon tests). [8–10]

Group differences in community composition (beta-diversity) were assessed using Bray–Curtis dissimilarities [11] (computed after Hellinger transformation of abundance profiles) [12] and tested using PERMANOVA (adonis2 in vegan) with permutation-based significance. [13–14] Ordination was performed by principal coordinates analysis (PCoA) on the Bray–Curtis distance matrix to visualize sample-to-sample relationships. [15]

Differential abundance testing was performed using DESeq2 (negative binomial GLM). [16] Across analyses involving multiple hypothesis tests, p-values were adjusted using the Benjamini–Hochberg false discovery rate procedure. [17] Pathway inference

Predicted functional potential (gene families and pathways) was inferred from 16S ASVs using PICRUSt2. [18] References

Illumina. 16S Metagenomic Sequencing Library Preparation (Part #15044223 Rev. B) [Internet]. Illumina; 2013. (Includes the overhang adapter primer structure and V3–V4 primer sequences).

Andrews S. FastQC: a quality control tool for high throughput sequence data [Internet]. Babraham Bioinformatics; 2010 [cited 2025 Dec 18]. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi:10.1038/nmeth.3869.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi:10.7717/peerj.2584.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–D596. doi:10.1093/nar/gks1219.

McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/journal.pone.0061217.

Wilcoxon F. Individual comparisons by ranking methods. Biometrics Bulletin. 1945;1(6):80–83. doi:10.2307/3001968.

Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J Am Stat Assoc. 1952;47:583–621. doi:10.1080/01621459.1952.10483441.

(If you want an additional general nonparametric/post-hoc reference beyond Wilcoxon/Kruskal–Wallis, tell me your preferred one and I’ll format it consistently.)

Bray JR, Curtis JT. An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr. 1957;27:325–349. doi:10.2307/1942268.

Legendre P, Gallagher ED. Ecologically meaningful transformations for ordination of species data. Oecologia. 2001;129(2):271–280. doi:10.1007/s004420100716.

Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46. doi:10.1111/j.1442-9993.2001.01070.pp.x.

Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, et al. vegan: Community Ecology Package [Internet]. R package. Available from: https://CRAN.R-project.org/package=vegan. doi:10.32614/CRAN.package.vegan.

Gower JC. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika. 1966;53(3–4):325–338. doi:10.1093/biomet/53.3-4.325.

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi:10.1186/s13059-014-0550-8.

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B. 1995;57(1):289–300. doi:10.1111/j.2517-6161.1995.tb02031.x.

Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38(6):685–688. doi:10.1038/s41587-020-0548-6. (slamo.biochem.dal.ca)

Phyloseq_Group9_10_11_pre-FMT.Rmd

author: “” date: ‘r format(Sys.time(), "%d %m %Y")‘ header-includes:

  • \usepackage{color, fancyvrb} output: rmdformats::readthedown: highlight: kate number_sections : yes pdf_document: toc: yes toc_depth: 2 number_sections : yes

    
#install.packages(c("picante", "rmdformats"))
#mamba install -c conda-forge freetype libpng harfbuzz fribidi
#mamba install -c conda-forge r-systemfonts r-svglite r-kableExtra freetype fontconfig harfbuzz fribidi libpng
library(knitr)
library(rmdformats)
library(readxl)
library(dplyr)
library(kableExtra)
library(openxlsx)
library(DESeq2)
library(writexl)

options(max.print="75")
knitr::opts_chunk$set(fig.width=8,
                    fig.height=6,
                    eval=TRUE,
                    cache=TRUE,
                    echo=TRUE,
                    prompt=FALSE,
                    tidy=FALSE,
                    comment=NA,
                    message=FALSE,
                    warning=FALSE)
opts_knit$set(width=85)
#rmarkdown::render('Phyloseq_Group9_10_11_pre-FMT.Rmd',output_file='Phyloseq_Group9_10_11_pre-FMT.html')
# Phyloseq R library
#* Phyloseq web site : https://joey711.github.io/phyloseq/index.html
#* See in particular tutorials for
#    - importing data: https://joey711.github.io/phyloseq/import-data.html
#    - heat maps: https://joey711.github.io/phyloseq/plot_heatmap-examples.html

    Data

    Import raw data and assign sample key:

    #extend qiime2_metadata_for_qza_to_phyloseq.tsv with Diet and Flora
#setwd("~/DATA/Data_Laura_16S_2/core_diversity_e4753")
#map_corrected <- read.csv("qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1)
#knitr::kable(map_corrected) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

    Prerequisites to be installed

    install.packages("dplyr")     # To manipulate dataframes
install.packages("readxl")    # To read Excel files into R
install.packages("ggplot2")   # for high quality graphics
install.packages("heatmaply")
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
    #mamba install -c conda-forge r-ggplot2 r-vegan r-data.table
#BiocManager::install("microbiome")
#install.packages("ggpubr")
#install.packages("heatmaply")
library("readxl") # necessary to import the data from Excel file
library("ggplot2") # graphics
library("picante")
library("microbiome") # data analysis and visualisation
library("phyloseq") # also the basis of data object. Data analysis and visualisation
library("ggpubr") # publication quality figures, based on ggplot2
library("dplyr") # data handling, filter and reformat data frames
library("RColorBrewer") # nice color options
library("heatmaply")
library(vegan)
library(gplots)
#install.packages("openxlsx")
library(openxlsx)

    Read the data and create phyloseq objects

    Three tables are needed

    • OTU
    • Taxonomy
    • Samples
    
  library(tidyr)

  # For QIIME1
  #ps.ng.tax <- import_biom("./exported_table/feature-table.biom", "./exported-tree/tree.nwk")

  # For QIIME2
  #install.packages("remotes")
  #remotes::install_github("jbisanz/qiime2R")
  #"core_metrics_results/rarefied_table.qza", rarefying performed in the code, therefore import the raw table.
  library(qiime2R)
  ps_raw <- qza_to_phyloseq(
    features =  "table.qza",  #cp ../Data_Karoline_16S_2025/dada2_tests2/test_7_f240_r240/table.qza .
    tree = "rooted-tree.qza",  #cp ../Data_Karoline_16S_2025/rooted-tree.qza .
    metadata = "qiime2_metadata_for_qza_to_phyloseq.tsv"  #cp ../Data_Karoline_16S_2025/qiime2_metadata_for_qza_to_phyloseq.tsv .
  )
  # or
  #biom convert \
  #      -i ./exported_table/feature-table.biom \
  #      -o ./exported_table/feature-table-v1.biom \
  #      --to-json
  #ps_raw <- import_biom("./exported_table/feature-table-v1.biom", treefilename="./exported-tree/tree.nwk")

  sample <- read.csv("./qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1)
  SAM = sample_data(sample, errorIfNULL = T)

  #> setdiff(rownames(SAM), sample_names(ps_raw))
  #[1] "sample-L9" should be removed since the low reads

  ps_base <- merge_phyloseq(ps_raw, SAM)
  print(ps_base)

  taxonomy <- read.delim("taxonomy.tsv", sep="\t", header=TRUE)  #cp ../Data_Karoline_16S_2025/exported-taxonomy/taxonomy.tsv .
  #head(taxonomy)
  # Separate taxonomy string into separate ranks
  taxonomy_df <- taxonomy %>% separate(Taxon, into = c("Domain","Phylum","Class","Order","Family","Genus","Species"), sep = ";", fill = "right", extra = "drop")
  # Use Feature.ID as rownames
  rownames(taxonomy_df) <- taxonomy_df$Feature.ID
  taxonomy_df <- taxonomy_df[, -c(1, ncol(taxonomy_df))]  # Drop Feature.ID and Confidence
  # Create tax_table
  tax_table_final <- phyloseq::tax_table(as.matrix(taxonomy_df))
  # Merge tax_table with existing phyloseq object
  ps_base <- merge_phyloseq(ps_base, tax_table_final)
  # Check
  ps_base

  #colnames(phyloseq::tax_table(ps_base)) <- c("Domain","Phylum","Class","Order","Family","Genus","Species")
  saveRDS(ps_base, "./ps_base.rds")

    Visualize data

    sample_names(ps_base)
rank_names(ps_base)
sample_variables(ps_base)

# Define sample names once
samples <- c(
  #"sample-A1","sample-A2","sample-A5","sample-A6","sample-A7","sample-A8","sample-A9","sample-A10",  #RESIZED: "sample-A3","sample-A4","sample-A11",
  #"sample-B1","sample-B2","sample-B3","sample-B4","sample-B5","sample-B6","sample-B7",  #RESIZED: "sample-B8","sample-B9","sample-B10","sample-B11","sample-B12","sample-B13","sample-B14","sample-B15","sample-B16",
  #"sample-C1","sample-C2","sample-C3","sample-C4","sample-C5","sample-C6","sample-C7",  #RESIZED: "sample-C8","sample-C9","sample-C10",
  #"sample-E1","sample-E2","sample-E3","sample-E4","sample-E5","sample-E6","sample-E7","sample-E8","sample-E9","sample-E10",  #RESIZED:
  #"sample-F1","sample-F2","sample-F3","sample-F4","sample-F5",
  "sample-G1","sample-G2","sample-G3","sample-G4","sample-G5","sample-G6",
  "sample-H1","sample-H2","sample-H3","sample-H4","sample-H5","sample-H6",
  "sample-I1","sample-I2","sample-I3","sample-I4","sample-I5","sample-I6",
  "sample-J1","sample-J2","sample-J3","sample-J4","sample-J10","sample-J11",  #RESIZED: "sample-J5","sample-J8","sample-J9",     "sample-J6","sample-J7",
  "sample-K1","sample-K2","sample-K3","sample-K4","sample-K5","sample-K6",  #RESIZED: "sample-K7","sample-K8","sample-K9","sample-K10",    "sample-K11","sample-K12","sample-K13","sample-K14","sample-K15",
  "sample-L2","sample-L3","sample-L4","sample-L5","sample-L6"  #RESIZED:"sample-L1","sample-L7","sample-L8","sample-L10","sample-L11","sample-L12","sample-L13","sample-L14","sample-L15",
  #"sample-M1","sample-M2","sample-M3","sample-M4","sample-M5","sample-M6","sample-M7","sample-M8",
  #"sample-N1","sample-N2","sample-N3","sample-N4","sample-N5","sample-N6","sample-N7","sample-N8","sample-N9","sample-N10",
  #"sample-O1","sample-O2","sample-O3","sample-O4","sample-O5","sample-O6","sample-O7","sample-O8"
)
ps_pruned <- prune_samples(samples, ps_base)

sample_names(ps_pruned)
rank_names(ps_pruned)
sample_variables(ps_pruned)

    No samples were excluded as low-depth outliers (library sizes below the minimum depth threshold of 1,000 reads), and the remaining dataset (ps_filt) contains only samples meeting this depth cutoff with taxa retained only if they have nonzero total counts.

    # ------------------------------------------------------------
#   Filter low-depth samples (recommended for all analyses)
# ------------------------------------------------------------
min_depth <- 1000  # <-- adjust to your data / study design, keeps all!
ps_filt <- prune_samples(sample_sums(ps_pruned) >= min_depth, ps_pruned)
ps_filt <- prune_taxa(taxa_sums(ps_filt) > 0, ps_filt)

# Keep a depth summary for reporting / QC
depth_summary <- summary(sample_sums(ps_filt))
depth_summary

    Differential abundance (DESeq2) → ps_deseq: non-rarefied integer counts derived from ps_filt, with optional count-based taxon prefilter (default: taxa total counts ≥ 10 across all samples)

    From ps_filt (e.g. 5669 taxa and 239 samples), we branch into analysis-ready objects in two directions:

    • Direction 1 for diversity analyses

  • Alpha diversity: ps_rarefied ✅ (common)

  • Beta diversity:

    • Unweighted UniFrac / Jaccard: ps_rarefied ✅ (often recommended)
    • Bray–Curtis / ordination on abundances: ps_rel or Hellinger ✅ (rarefaction optional)
    • Aitchison (CLR): CLR-transformed (non-rarefied) ✅ (no rarefaction)

    Normalize number of reads in each sample using median sequencing depth.

    
# RAREFACTION
set.seed(9242)  # This will help in reproducing the filtering and nomalisation.
ps_rarefied <- rarefy_even_depth(ps_filt, sample.size = 6389)
#total <- 6389

# # NORMALIZE number of reads in each sample using median sequencing depth.
# total = median(sample_sums(ps.ng.tax))
# #> total
# #[1] 42369
# standf = function(x, t=total) round(t * (x / sum(x)))
# ps.ng.tax = transform_sample_counts(ps.ng.tax, standf)
# ps_rel <- microbiome::transform(ps.ng.tax, "compositional")
#
# saveRDS(ps.ng.tax, "./ps.ng.tax.rds")
    • Direction 2 for taxonomic composition plots

  • Taxonomic composition → ps_rel: relative abundance (compositional) computed after sample filtering (e.g. 5669 taxa and 239 samples)

  • Optional cleaner composition plots → ps_abund / ps_abund_rel: taxa filtered for plotting (e.g., keep taxa with mean relative abundance > 0.1%); (e.g. 95 taxa and 239 samples) ps_abund = counts, ps_abund_rel = relative abundance (use for visualization, not DESeq2)

    For the heatmaps, we focus on the most abundant OTUs by first converting counts to relative abundances within each sample. We then filter to retain only OTUs whose mean relative abundance across all samples exceeds 0.1% (0.001). We are left with 199 OTUs which makes the reading much more easy.

    # 1) Convert to relative abundances
ps_rel <- transform_sample_counts(ps_filt, function(x) x / sum(x))

# 2) Get the logical vector of which OTUs to keep (based on relative abundance)
keep_vector <- phyloseq::filter_taxa(
ps_rel,
function(x) mean(x) > 0.001,
prune = FALSE
)

# 3) Use the TRUE/FALSE vector to subset absolute abundance data
ps_abund <- prune_taxa(names(keep_vector)[keep_vector], ps_filt)

# 4) Normalize the final subset to relative abundances per sample
ps_abund_rel <- transform_sample_counts(
ps_abund,
function(x) x / sum(x)
)
    library(stringr)
#for id in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100  101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206; do
#for id in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62; do
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"], \"__\")[[1]][2]"
#done
phyloseq::tax_table(ps_abund_rel)[1,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[96,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[96,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[97,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[97,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[98,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[98,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[99,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[99,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[100,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[100,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[101,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[101,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[102,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[102,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[103,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[103,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[104,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[104,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[105,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[105,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[106,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[106,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[107,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[107,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[108,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[108,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[109,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[109,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[110,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[110,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[111,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[111,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[112,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[112,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[113,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[113,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[114,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[114,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[115,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[115,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[116,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[116,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[117,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[117,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[118,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[118,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[119,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[119,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[120,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[120,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[121,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[121,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[122,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[122,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[123,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[123,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[124,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[124,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[125,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[125,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[126,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[126,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[127,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[127,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[128,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[128,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[129,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[129,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[130,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[130,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[131,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[131,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[132,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[132,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[133,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[133,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[134,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[134,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[135,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[135,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[136,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[136,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[137,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[137,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[138,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[138,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[139,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[139,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[140,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[140,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[141,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[141,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[142,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[142,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[143,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[143,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[144,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[144,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[145,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[145,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[146,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[146,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[147,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[147,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[148,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[148,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[149,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[149,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[150,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[150,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[151,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[151,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[152,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[152,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[153,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[153,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[154,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[154,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[155,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[155,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[156,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[156,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[157,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[157,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[158,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[158,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[159,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[159,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[160,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[160,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[161,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[161,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[162,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[162,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[163,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[163,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[164,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[164,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[165,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[165,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[166,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[166,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[167,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[167,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[168,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[168,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[169,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[169,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[170,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[170,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[171,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[171,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[172,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[172,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[173,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[173,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[174,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[174,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[175,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[175,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[176,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[176,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[177,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[177,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[178,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[178,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[179,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[179,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[180,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[180,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[181,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[181,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[182,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[182,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[183,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[183,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[184,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[184,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[185,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[185,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[186,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[186,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[187,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[187,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[188,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[188,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[189,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[189,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[190,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[190,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[191,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[191,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[192,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[192,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[193,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[193,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[194,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[194,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[195,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[195,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[196,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[196,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[197,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[197,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[198,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[198,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[199,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[199,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[200,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[200,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[201,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[201,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[202,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[202,"Species"], "__")[[1]][2]

    Taxonomic summary

    Bar plots in phylum level

    
#aes(color="Phylum", fill="Phylum") --> aes()
#ggplot(data=data, aes(x=Sample, y=Abundance, fill=Phylum))
#options(max.print = 1e6)
my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
plot_bar(ps_abund_rel, fill="Phylum") + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=2))                                  #6 instead of theme.size

    \pagebreak Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

    ps_abund_rel_group <- merge_samples(ps_abund_rel, "G9_10_11_preFMT")
#PENDING: The effect weighted twice by sum(x), is the same to the effect weighted once directly from absolute abundance?!
ps_abund_rel_group_ = transform_sample_counts(ps_abund_rel_group, function(x) x / sum(x))
#plot_bar(ps_abund_relSampleType_, fill = "Phylum") + geom_bar(aes(color=Phylum, fill=Phylum), stat="identity", position="stack")

plot_bar(ps_abund_rel_group_, fill="Phylum") +
geom_bar(stat="identity", position="stack") +
scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
scale_fill_manual(values = my_colors) +
theme(
  axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
  axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
  axis.title.x = element_text(size = 12, colour = "black"),
  axis.title.y = element_text(size = 12, colour = "black")
)

    Bar plots in class level

    my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
plot_bar(ps_abund_rel, fill="Class") + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=3))

    Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

    plot_bar(ps_abund_rel_group_, fill="Class") +
geom_bar(stat="identity", position="stack") +
scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
scale_fill_manual(values = my_colors) +
theme(
  axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
  axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
  axis.title.x = element_text(size = 12, colour = "black"),
  axis.title.y = element_text(size = 12, colour = "black")
)

    \pagebreak

    Bar plots in order level

    my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
plot_bar(ps_abund_rel, fill="Order") + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=4))

    Regroup together pre vs post stroke and normalize number of reads in each group using median sequencing depth.

    plot_bar(ps_abund_rel_group_, fill="Order") +
geom_bar(stat="identity", position="stack") +
scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
scale_fill_manual(values = my_colors) +
theme(
  axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
  axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
  axis.title.x = element_text(size = 12, colour = "black"),
  axis.title.y = element_text(size = 12, colour = "black")
)

    \pagebreak

    Bar plots in family level

    my_colors <- c(
        "#FF0000", "#000000", "#0000FF", "#C0C0C0", "#FFFFFF", "#FFFF00", "#00FFFF", "#FFA500", "#00FF00", "#808080", "#FF00FF", "#800080", "#FDD017", "#0000A0", "#3BB9FF", "#008000", "#800000", "#ADD8E6", "#F778A1", "#800517", "#736F6E", "#F52887", "#C11B17", "#5CB3FF", "#A52A2A", "#FF8040", "#2B60DE", "#736AFF", "#1589FF", "#98AFC7", "#8D38C9", "#307D7E", "#F6358A", "#151B54", "#6D7B8D", "#FDEEF4", "#FF0080", "#F88017", "#2554C7", "#FFF8C6", "#D4A017", "#306EFF", "#151B8D", "#9E7BFF", "#EAC117", "#E0FFFF", "#15317E", "#6C2DC7", "#FBB917", "#FCDFFF", "#15317E", "#254117", "#FAAFBE", "#357EC7"
      )
plot_bar(ps_abund_rel, fill="Family") + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = my_colors) + theme(axis.text = element_text(size = 7, colour="black")) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=8))

    Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.

    plot_bar(ps_abund_rel_group_, fill="Family") +
geom_bar(stat="identity", position="stack") +
scale_x_discrete(limits = c("pre-FMT", "Group9","Group10","Group11")) +
scale_fill_manual(values = my_colors) +
theme(
  axis.text.x  = element_text(angle = 30, hjust = 1, vjust = 1, size = 11, colour = "black"),
  axis.text.y  = element_text(angle = 0,  size = 11, colour = "black"),
  axis.title.x = element_text(size = 12, colour = "black"),
  axis.title.y = element_text(size = 12, colour = "black")
)

    \pagebreak

    \pagebreak

    Alpha diversity

    Plot Chao1 richness estimator, Observed OTUs, Shannon index, and Phylogenetic diversity. Regroup together samples from the same group.

    # using rarefied data
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even42369.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_stool/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_swab/rep_set.tre

library(dplyr)
library(reshape2)
library(ggpubr)
library(phyloseq)
library(kableExtra)

# ------------------------------------------------------------
# 0) Restrict analysis to the specified sample subset
# ------------------------------------------------------------
stopifnot(exists("samples"))
stopifnot(exists("ps_rarefied"))

ps_rarefied_sub <- prune_samples(samples, ps_rarefied)

hmp.meta <- meta(ps_rarefied_sub)
hmp.meta$sam_name <- rownames(hmp.meta)

# ------------------------------------------------------------
# 1) Read QIIME2 alpha-diversity outputs
# ------------------------------------------------------------
shannon  <- read.table("exported_alpha/shannon/alpha-diversity.tsv",
                    header = TRUE, sep = "\t", stringsAsFactors = FALSE)
faith_pd <- read.table("exported_alpha/faith_pd/alpha-diversity.tsv",
                    header = TRUE, sep = "\t", stringsAsFactors = FALSE)
observed <- read.table("exported_alpha/observed_features/alpha-diversity.tsv",
                    header = TRUE, sep = "\t", stringsAsFactors = FALSE)

colnames(shannon)  <- c("sam_name", "shannon")
colnames(faith_pd) <- c("sam_name", "PD_whole_tree")
colnames(observed) <- c("sam_name", "observed_otus")

div.df <- Reduce(function(x, y) merge(x, y, by = "sam_name", all = FALSE),
              list(shannon, faith_pd, observed))

# ------------------------------------------------------------
# 2) Merge in metadata (from the pruned phyloseq object)
# ------------------------------------------------------------
div.df <- merge(div.df, hmp.meta, by = "sam_name", all.x = TRUE, all.y = FALSE)

# Keep ONLY samples from the predefined list (safety net)
div.df <- div.df %>% filter(sam_name %in% samples)

# ------------------------------------------------------------
# 3) Collapse groups: Group6/7/8 -> pre-FMT; keep only 4 groups
# ------------------------------------------------------------
div.df <- div.df %>%
mutate(
  Group4 = case_when(
    Group %in% c("Group6","Group7","Group8") ~ "pre-FMT",
    Group %in% c("Group9","Group10","Group11") ~ as.character(Group),
    TRUE ~ NA_character_
  ),
  Group4 = factor(Group4, levels = c("pre-FMT","Group9","Group10","Group11"))
) %>%
filter(!is.na(Group4))

# ------------------------------------------------------------
# 4) Reformat table for reporting
# ------------------------------------------------------------
div.df2 <- div.df[, c("sam_name", "Group4", "shannon", "observed_otus", "PD_whole_tree")]
colnames(div.df2) <- c("Sample name", "Group", "Shannon", "OTU", "Phylogenetic Diversity")

write.csv(div.df2, file = "alpha_diversities_G9_10_11_preFMT.csv", row.names = FALSE)

#knitr::kable(div.df2) %>%
#  kable_styling(bootstrap_options = c("striped","hover","condensed","responsive"))

# ------------------------------------------------------------
# 5) QC: print which samples were used
# ------------------------------------------------------------
requested_samples <- samples
present_in_ps <- sample_names(ps_rarefied)

missing_in_ps <- setdiff(requested_samples, present_in_ps)

cat("\n==== QC: Sample selection (ps_rarefied) ====\n")
cat("Requested samples:", length(requested_samples), "\n")
cat("Present in ps_rarefied:", length(present_in_ps), "\n")
cat("Missing from ps_rarefied:", length(missing_in_ps), "\n")
if (length(missing_in_ps) > 0) print(missing_in_ps)

used_samples <- div.df2$`Sample name`
missing_in_alpha <- setdiff(requested_samples, used_samples)
extra_in_alpha <- setdiff(used_samples, requested_samples)

cat("\n==== QC: Samples used in alpha-div df (div.df2) ====\n")
cat("Used samples:", length(used_samples), "\n")
cat("Requested but NOT used:", length(missing_in_alpha), "\n")
if (length(missing_in_alpha) > 0) print(missing_in_alpha)
cat("Used but NOT requested (should be 0):", length(extra_in_alpha), "\n")
if (length(extra_in_alpha) > 0) print(extra_in_alpha)

qc_table <- div.df %>%
select(sam_name, Group, Group4) %>%
distinct() %>%
arrange(Group4, Group, sam_name)

#cat("\n==== QC: Sample -> Group mapping used for plotting ====\n")
#print(qc_table)
#
#cat("\n==== QC: Counts per collapsed group (Group4) ====\n")
#print(div.df$Group4)

# ------------------------------------------------------------
# 6) Melt + plot
# ------------------------------------------------------------
div_df_melt <- reshape2::melt(
div.df2,
id.vars = c("Sample name","Group"),
variable.name = "variable",
value.name = "value"
)

# ensure final group order
div_df_melt$Group <- factor(div_df_melt$Group, levels = c("pre-FMT","Group9","Group10","Group11"))

#p <- ggboxplot(div_df_melt, x = "Group", y = "value",
#               facet.by = "variable",
#               scales = "free",
#               width = 0.5,
#               fill = "gray", legend = "right") +
#  theme(
#    axis.text.x  = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
#    axis.text.y  = element_text(size = 10),
#    axis.title.x = element_text(size = 12),
#    axis.title.y = element_text(size = 12)
#  )
# all pairwise comparisons among the 4 groups
#lev <- levels(droplevels(div_df_melt$Group))
#L.pairs <- combn(lev, 2, simplify = FALSE)
#
#p2 <- p + stat_compare_means(
#  method = "wilcox.test",
#  comparisons = L.pairs,
#  label = "p.signif",
#  p.adjust.method = "BH",
#  hide.ns = FALSE,
#  symnum.args = list(
#    cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1),
#    symbols   = c("****", "***", "**", "*", "ns")
#  )
#)
#p2

# ------------------------------------------------------------
# 7) Save figure
# ------------------------------------------------------------
#ggsave("./figures/alpha_diversity_G9_10_11_preFMT.png", p2, device="png", height = 10, width = 15, dpi = 300)
#ggsave("./figures/alpha_diversity_G9_10_11_preFMT.svg", p2, device="svg", height = 10, width = 15)

# ------------------------------------------------------------
# 8) Save statistics
# ------------------------------------------------------------

library(dplyr)
library(purrr)

# same pair list as in the plot
lev <- levels(droplevels(div_df_melt$Group))
L.pairs <- combn(lev, 2, simplify = FALSE)

# Pairwise Wilcoxon per metric, with BH adjustment (matches p.adjust.method="BH")
stats_for_plot <- div_df_melt %>%
group_by(variable) %>%
group_modify(~{
  dat <- .x

  res <- purrr::map_dfr(L.pairs, function(pr) {
    g1 <- pr[1]; g2 <- pr[2]
    x1 <- dat$value[dat$Group == g1]
    x2 <- dat$value[dat$Group == g2]

    wt <- suppressWarnings(wilcox.test(x1, x2, exact = FALSE))

    tibble(
      group1 = g1,
      group2 = g2,
      n1 = length(x1),
      n2 = length(x2),
      p = unname(wt$p.value)
    )
  })

  res %>%
    mutate(
      p.adj = p.adjust(p, method = "BH"),
      p.signif = case_when(
        p.adj <= 0.0001 ~ "****",
        p.adj <= 0.001  ~ "***",
        p.adj <= 0.01   ~ "**",
        p.adj <= 0.05   ~ "*",
        TRUE            ~ "ns"
      )
    )
}) %>%
ungroup() %>%
rename(Metric = variable) %>%
arrange(Metric, group1, group2)

# Print the exact statistics used for annotation
print(stats_for_plot, n = Inf)

write.csv(stats_for_plot, "./figures/alpha_diversity_pairwise_stats_used_for_plot.csv", row.names = FALSE)

library(openxlsx)

# (optional) make sure the folder exists
dir.create("./figures", showWarnings = FALSE, recursive = TRUE)

out_xlsx <- "./figures/alpha_diversity_pairwise_stats_used_for_plot.xlsx"

write.xlsx(
x = list("pairwise_stats" = stats_for_plot),
file = out_xlsx,
overwrite = TRUE
)

cat("Saved Excel file to: ", out_xlsx, "\n", sep = "")
    # ---------------------------------------------------------------------------------
# ----------------------------- draw plots from input -----------------------------

library(dplyr)
library(ggpubr)
library(reshape2)

# Example: read from a CSV file you wrote earlier
# stats_for_plot <- read.csv("./figures/alpha_diversity_pairwise_stats_used_for_plot.csv", stringsAsFactors = FALSE)

# Or if you paste as text:
txt <- 'Metric,group1,group2,n1,n2,p,p.adj,p.signif
Shannon,Group10,Group11,6,5,1,1,ns
Shannon,Group9,Group10,6,6,0.297953061608168,0.595906123216336,ns
Shannon,Group9,Group11,6,5,0.522816653919089,0.631819188094748,ns
Shannon,pre-FMT,Group10,18,6,0.017949090591566,0.0538472717746981,ns
Shannon,pre-FMT,Group11,18,5,0.00651735384842052,0.0391041230905231,*
Shannon,pre-FMT,Group9,18,6,0.526515990078957,0.631819188094748,ns
OTU,Group10,Group11,6,5,0.143214612017615,0.214821918026422,ns
OTU,Group9,Group10,6,6,0.229766270461138,0.275719524553366,ns
OTU,Group9,Group11,6,5,0.522816653919089,0.522816653919089,ns
OTU,pre-FMT,Group10,18,6,0.0015274145728676,0.00916448743720559,**
OTU,pre-FMT,Group11,18,5,0.0675601586409843,0.135120317281969,ns
OTU,pre-FMT,Group9,18,6,0.00759484512604444,0.0227845353781333,*
Phylogenetic Diversity,Group10,Group11,6,5,1,1,ns
Phylogenetic Diversity,Group9,Group10,6,6,1,1,ns
Phylogenetic Diversity,Group9,Group11,6,5,0.927264473525232,1,ns
Phylogenetic Diversity,pre-FMT,Group10,18,6,0.000361550896811121,0.00108465269043336,**
Phylogenetic Diversity,pre-FMT,Group11,18,5,0.000910436385913111,0.00182087277182622,**
Phylogenetic Diversity,pre-FMT,Group9,18,6,0.000361550896811121,0.00108465269043336,**'

stats_for_plot <- read.csv(textConnection(txt), stringsAsFactors = FALSE)

# Match naming to your plot data: your facet variable is called "variable"
stats_for_plot <- stats_for_plot %>%
rename(variable = Metric) %>%
mutate(
  group1 = factor(group1, levels = c("pre-FMT","Group9","Group10","Group11")),
  group2 = factor(group2, levels = c("pre-FMT","Group9","Group10","Group11"))
)

# ------------------------------------------------------------
# Melt + plot (same as yours)
# ------------------------------------------------------------
div_df_melt <- reshape2::melt(
div.df2,
id.vars = c("Sample name","Group"),
variable.name = "variable",
value.name = "value"
)

div_df_melt$Group <- factor(div_df_melt$Group, levels = c("pre-FMT","Group9","Group10","Group11"))

p <- ggboxplot(div_df_melt, x = "Group", y = "value",
            facet.by = "variable",
            scales = "free",
            width = 0.5,
            fill = "gray", legend = "right") +
theme(
  axis.text.x  = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
  axis.text.y  = element_text(size = 10),
  axis.title.x = element_text(size = 12),
  axis.title.y = element_text(size = 12)
)

# ------------------------------------------------------------
# Add significance from your table (NO recomputation)
# ------------------------------------------------------------

# Compute y positions per facet so brackets don't overlap
ymax_by_metric <- div_df_melt %>%
group_by(variable) %>%
summarise(ymax = max(value, na.rm = TRUE), .groups = "drop")

stats_for_plot2 <- stats_for_plot %>%
left_join(ymax_by_metric, by = "variable") %>%
group_by(variable) %>%
arrange(p.adj) %>%
mutate(
  # stack brackets within each facet
  y.position = ymax * (1.05 + 0.08 * (row_number() - 1)),
  # what to display (stars or "ns")
  label = p.signif
) %>%
ungroup()

p2 <- p +
stat_pvalue_manual(
  stats_for_plot2,
  label = "label",
  xmin = "group1",
  xmax = "group2",
  y.position = "y.position",
  tip.length = 0.01,
  hide.ns = FALSE
)

p2

# ------------------------------------------------------------
# Save
# ------------------------------------------------------------
ggsave("./figures/alpha_diversity_G9_10_11_preFMT_from_table.png",
    p2, device="png", height = 6, width = 9, dpi = 300)
ggsave("./figures/alpha_diversity_G9_10_11_preFMT_from_table.svg",
    p2, device="svg", height = 6, width = 9)
# label = sprintf("BH p=%.3g", p.adj)

    Beta-diversity

    Pairwise PERMANOVA tests

    Pairwise PERMANOVA tests were performed on Bray–Curtis distance matrices to compare bacterial community composition between all pairs of sample groups (metadata column Group). For each pairwise comparison, the distance matrix was subset to samples from the two groups only, and significance was assessed using vegan::adonis2 with 9,999 permutations. Resulting p-values were adjusted for multiple testing using both Benjamini–Hochberg (BH/FDR) and Bonferroni corrections.

    Bray_pairwise_PERMANOVA <- read.csv("figures_MP_Group9_10_11_PreFMT/Bray_pairwise_PERMANOVA.csv", sep = ",")
knitr::kable(Bray_pairwise_PERMANOVA, caption = "Pairwise PERMANOVA results (distance-based community differences among Group levels).") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

    Global PERMANOVA on the weighted UniFrac distance matrix

    Groups 9, 10, 11 vs the mixed pre-FMT group

    # --- Global beta-diversity (PERMANOVA) ---
cat("```text\n")
cat(
"[PERMANOVA result]\n",
"The object contained internal attribute: PCoA ADONIS\n",
"Permutation test for adonis under reduced model\n",
"Permutation: free\n",
"Number of permutations: 9999\n",
"\n",
"vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)\n",
"         Df SumOfSqs      R2      F Pr(>F)    \n",
"Model     3   5.3256 0.58559 14.602  1e-04 ***\n",
"Residual 31   3.7689 0.41441                  \n",
"Total    34   9.0945 1.00000                  \n",
"---\n",
"Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1\n",
sep = ""
)
cat("```\n")

    Groups 9, 10, 11

    # --- Global beta-diversity (PERMANOVA) ---
cat("```text\n")
cat(
"[PERMANOVA result]\n",
"The object contained internal attribute: PCoA ADONIS\n",
"Permutation test for adonis under reduced model\n",
"Permutation: free\n",
"Number of permutations: 9999\n",
"\n",
"vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)\n",
"         Df SumOfSqs     R2      F Pr(>F)    \n",
"Model     2  0.82208 0.3324 3.4853  1e-04 ***\n",
"Residual 14  1.65109 0.6676                  \n",
"Total    16  2.47317 1.0000                  \n",
"---\n",
"Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1\n",
sep = ""
)
cat("```\n")

    Principal coordinates analysis (PCoA) based on Bray–Curtis dissimilarity

    Groups 9, 10, 11 vs the mixed pre-FMT group

    knitr::include_graphics("figures_MP_Group9_10_11_PreFMT/PCoA3.png")

    Groups 9, 10, 11

    knitr::include_graphics("figures_MP_Group9_10_11/PCoA3.png")

    Differential abundance analysis

    Differential abundance analysis aims to find the differences in the abundance of each taxa between two groups of samples, assigning a significance value to each comparison.

    Group 9 vs Group 10

    
# ------------------------------------------------------------
#  DESeq2: non-rarefied integer counts + optional taxon prefilter
# ------------------------------------------------------------
ps_deseq <- ps_filt

ps_deseq_sel2 <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel2) <- otu_table(ps_deseq)[,c("sample-J1","sample-J2","sample-J3","sample-J4","sample-J10","sample-J11",  "sample-K1","sample-K2","sample-K3","sample-K4","sample-K5","sample-K6")]
diagdds = phyloseq_to_deseq2(ps_deseq_sel2, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group9")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel2)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group9_vs_Group10"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
  scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
geom_point(aes(size = padj)) +
scale_size_continuous(name = "padj", range = c(8, 4)) +
theme_bw() +
theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
              width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
              width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics("DEGs_Group9_vs_Group10.png")

R Workflow for Family-Level Taxonomic Dendrograms (Benakis et al. Figure 1C Style)

Leave a reply
  1. A ready-to-run, clean R script that builds a family-level taxonomic dendrogram filtered by abundance (> 1%), following the same logic as Benakis et al. (Figure 1C).
  2. A Methods section formatted for inclusion in a manuscript, describing the same procedure in scientific writing style.

1. Ready-to-Run R Script

(Taxonomic dendrogram of microbial families filtered by relative abundance > 1%)

###############################################################################
# Taxonomic dendrogram of microbial families (abundance > 1%)
# Based on the Benakis et al. Figure 1C approach
# Author: [Your Name]
# Date: [Insert Date]
###############################################################################

# Load libraries
library(phyloseq)
library(dplyr)
library(tibble)
library(igraph)
library(ggraph)

# ------------------------------
# Step 1 — Agglomerate to Family level
# ------------------------------
# Assumes an existing phyloseq object: ps_filt

ps_fam <- tax_glom(ps_filt, taxrank = "Family", NArm = TRUE)
ps_fam <- prune_taxa(taxa_sums(ps_fam) > 0, ps_fam)

# Optional: restrict to selected groups if needed
# ps_fam <- subset_samples(ps_fam, Group %in% c("pre-FMT", "9", "10", "11"))

# ------------------------------
# Step 2 — Calculate relative abundance and filter families >1%
# ------------------------------

# Transform to relative abundance
ps_fam_relab <- transform_sample_counts(ps_fam, function(x) x / sum(x))

# Compute mean relative abundance across all samples
mean_abund <- taxa_sums(ps_fam_relab) / nsamples(ps_fam_relab)

# Keep only families with >1% mean relative abundance
keep_taxa <- names(mean_abund[mean_abund > 0.01])
ps_fam_top <- prune_taxa(keep_taxa, ps_fam_relab)

# ------------------------------
# Step 3 — Build taxonomic hierarchy (Phylum → Class → Order → Family)
# ------------------------------

tax <- as.data.frame(tax_table(ps_fam_top)) %>%
  rownames_to_column("taxa_id") %>%
  select(Phylum, Class, Order, Family) %>%
  mutate(across(everything(), as.character)) %>%
  distinct()

edges <- bind_rows(
  tax %>% transmute(from = Phylum, to = Class),
  tax %>% transmute(from = Class,  to = Order),
  tax %>% transmute(from = Order,  to = Family)
) %>%
  distinct() %>%
  filter(!is.na(from), !is.na(to), from != "", to != "")

# ------------------------------
# Step 4 — Plot dendrogram-style taxonomy tree
# ------------------------------

g <- graph_from_data_frame(edges, directed = TRUE)

p <- ggraph(g, layout = "dendrogram") +
  geom_edge_diagonal(color = "grey60") +
  geom_node_point(size = 2, color = "steelblue") +
  geom_node_text(aes(label = name), hjust = -0.1, size = 3) +
  theme_void() +
  coord_flip() +
  ggtitle("Taxonomic dendrogram of microbial families (>1% abundance)")

print(p)

# ------------------------------
# Optional: collapse remaining rare families as "Other"
# ------------------------------
# This can be done before filtering or directly in the figure annotation
###############################################################################

2. Methods Section (for Manuscript)

Taxonomic Dendrogram Construction

A taxonomic dendrogram illustrating the microbial composition at the family level was generated in R (version 4.3.0) using the phyloseq and ggraph packages. The analysis followed an approach similar to that presented by Benakis et al. (2020, Cell Host \& Microbe, Figure 1C).

First, the filtered amplicon sequence variant (ASV) table was agglomerated to the Family rank using the tax_glom() function from phyloseq. The dataset was then transformed to relative abundances for each sample, and families with a mean relative abundance greater than 1% across all samples were retained for visualization. Families below this threshold were excluded and considered part of the “Other” category for interpretability.

A hierarchical taxonomy table (Phylum → Class → Order → Family) was extracted, and edges representing parent–child relationships were assembled using dplyr. The resulting taxonomic relationships were converted into a directed graph structure using igraph, and visualized as a dendrogram with ggraph (layout = "dendrogram").

This approach provides a qualitative overview of microbial family-level diversity while reducing visual noise from rare taxa, consistent with the display strategy used in the original publication.

Would you like me to adapt the Methods version to a more formal journal submission style (e.g., third person passive voice and APA-compliant citation format)?

Generating a Taxonomic Dendrogram of Significant Microbial Families in R (Based on Benakis et al. Figure 1C)

Concept overview

Yes—this is doable in R, and you can restrict the dendrogram to only significant microbial families. Based on the structure in the Benakis et al. paper:

  • Figure 1C is a taxonomic dendrogram (Phylum → Class → Order → Family), not a clustering of samples.
  • The authors filtered families by frequency > 1%, not by statistical significance.

If your PI asks for “only significantly expressed families,” you first need to perform a differential abundance test at the Family level (e.g., using ANCOM-BC2 or DESeq2) before plotting only those families or highlighting them on the tree.

Recommended Workflow

Step 1 — Agglomerate to Family level (phyloseq)

library(phyloseq)

ps_fam <- tax_glom(ps_filt, taxrank = "Family", NArm = TRUE)
ps_fam <- prune_taxa(taxa_sums(ps_fam) > 0, ps_fam)

# Restrict to requested sample groups
ps_fam_sub <- subset_samples(ps_fam, Group %in% c("9", "10", "11", "pre-FMT"))
sample_data(ps_fam_sub)$Group <- factor(sample_data(ps_fam_sub)$Group,
                                       levels = c("pre-FMT", "9", "10", "11"))

Step 2 — Differential abundance to define significant families

Option A: ANCOM-BC2 (recommended for microbiome data)

library(ANCOMBC)

an2 <- ancombc2(data = ps_fam_sub,
                formula = "Group",
                p_adj_method = "BH",
                prv_cut = 0, lib_cut = 0,
                group = "Group",
                global = FALSE)

res <- an2$res
# Inspect results: names(an2$res), matrices such as res$diff_abn and res$q_val

Option B: DESeq2 (alternative)

library(DESeq2)

dds <- phyloseq_to_deseq2(ps_fam_sub, ~ Group)
dds <- DESeq(dds)

# Example contrast: Group 9 vs 10
r_9_10 <- results(dds, contrast = c("Group", "9", "10"))
sig_9_10 <- rownames(r_9_10)[which(r_9_10$padj < 0.05)]
sig_9_10 <- sig_9_10[!is.na(sig_9_10)]

Decide what “significant” means for your plot:

  • Only families significant for 9 vs 10, or
  • Families significant in any pairwise comparison among (9, 10, 11, pre-FMT).

Step 3 — Build the taxonomic dendrogram (Phylum → Class → Order → Family)

library(dplyr)
library(tibble)
library(igraph)
library(ggraph)

# Choose your significant taxa list (example from DESeq2)
sig_taxa <- sig_9_10

# Get taxonomy for significant families
tax <- as.data.frame(tax_table(ps_fam_sub)) %>%
  rownames_to_column("taxa_id") %>%
  filter(taxa_id %in% sig_taxa) %>%
  select(Phylum, Class, Order, Family) %>%
  mutate(across(everything(), as.character)) %>%
  distinct()

# Build hierarchical edges
edges <- bind_rows(
  tax %>% transmute(from = Phylum, to = Class),
  tax %>% transmute(from = Class,  to = Order),
  tax %>% transmute(from = Order,  to = Family)
) %>%
  distinct() %>%
  filter(!is.na(from), !is.na(to), from != "", to != "")

# Build graph
g <- graph_from_data_frame(edges, directed = TRUE)

# Plot dendrogram
p <- ggraph(g, layout = "dendrogram") +
  geom_edge_diagonal() +
  geom_node_point(size = 2) +
  geom_node_text(aes(label = name), hjust = -0.1, size = 3) +
  theme_void() +
  coord_flip()

p

Highlighting significance in the plot

To color families by direction (e.g., enriched in Group 9 vs 10), merge the log2FoldChange results from DESeq2 with the node names and use scale_color_gradient2() or similar in ggraph to map significance.

Summary for your report (Q1.5 suggested answer)

Yes—this can be done in R. The template figure in the Benakis paper shows a taxonomy-based dendrogram (Phylum → Class → Order → Family). In that study, families were filtered by abundance (only > 1% frequency) rather than statistical significance.

For our dataset, we can (i) construct the full family-level taxonomy tree and (ii) optionally restrict or highlight only those families that are significantly different between groups based on differential abundance testing (using DESeq2 or ANCOM-BC2 with Benjamini–Hochberg-adjusted p-values).

If you specify which comparison defines “significant” (only 9 vs 10 or across all four groups), the exact filtering and visualization code can be tailored to more closely match Figure 1C, including the “Other” bin and legend style.

MicrobiotaProcess.R for Data_Childrensclinic_16S_2025

Leave a reply 
## =========================================================
## MicrobiotaProcess_UPDATED.R
## Uses your objects:
##   - ps_filt        : for alpha + beta diversity (NOT taxa-filtered)
##   - ps_abund_rel   : for cleaner composition plots (taxa filtered for plotting)
##
## Output:
##   - Rarefaction curves + alpha diversity plots
##   - Bray (Hellinger) distance + PCoA + PERMANOVA
##   - Composition plots (Class) + heatmaps (from ps_abund_rel)
## =========================================================

## -----------------------------
## 0) Define groups (sample IDs)  ---- EXACTLY as provided
Group1<-c("U24080201","U25020701","O23092004","U24101801","U25022101","O23102703","A24062801","O23112205","U23071901","A23112002","U24111801","O23110101","U24121801","O23120101","O24011202","O23090803","A23060602","A24030402","U25011701","O24011901","U23090801","O24011201","O24011003","O23092202","O23082301","O23091403","O23112901","O23092201","O24013103","O24021403","O24010402","O23092005","O23092203","O24010302","O23090701","O23091501","O23092701","O24022202","O23092802","O23090601","O23100401","O24022102","O23081801","O23092006","O23100503","O23090602","O24013104","O24020803","O24010301","O24010404","O23090802","O23092801","O24022801","O23100706","O23102602","O24021601","O24012401","O24021603","O24022901","O24021501","O23110902","O23102601","O23102704","O23100803","O23102701","O24021401","O24022101","O24030603","O23110901","O23110903","O23110301","O24022301","O23102502","O23111501","O23111602","O24020705","O24021502","O24022201","O23110202","O23090801")

Group2<-c("U23071701","U23052401","U23052201","U24070401","O24011801","O23092003","A24071901","A24072901","O24011102","O23121501","O23092104","O23092001","O23121301","O24020701","O23112201","O23100701","O23100801","O24020903","O24020901","O24020703","O23112204")

Group3<-c("O23100802","O24011205","O23092002","O24011207","O23092103","O23102501","O24011005","A24030401","O24011004","A23051102","U25011702","O24011204","O23121502","O23120702","O24011206","O24021404","O23092101","O24010403","O23112303","O23083001","O23082302","O24010401","O24022302","O24010501","O23112902","O23082303","O23083102","O24013101","O23100402","O24020801","O23120701","O23121304","O24021602","O24011802","O23121306","O23120103","O24020905","O24012403","O24013102","O24021503","O24020904","O23102504","O24013105","O24030601","O23100705","O24030604","O23111601","O24020103","O24030602","O23110302","O23102603","O24031304","O24021402","O24020101","O24012501","O24020804","O23100804","O23102503","O24022902","O24020704","O23110904","O24020102","O24012402","O23102702","O23102604","O23110204","O23110203","O23083101","O23092702")

Group4<-c("O23112304","A23051103","A24071701","A23080101","A24031201","A24080201","O24011105","O23091305","O23121302","O23092803")

Group5<-c("O23091303","O23112301","O24011203","A23112001","O24011001","O24011002","O23091302","O24020902","O23092102","O23091401","O23121503","O23091402","O24020702","O23091301","O23112206","O24011103","O23121305","O24011101","O23121303","O24011104","O23120104","O23100704","O23112302","O23112203","O23100703","O24020805","O24020802","O23112202","O24031302","O23111502","O23100702","O24031301","O24031305","O23082402")

NTC<-c("NTC_2","NTC_3","NTC_16","NTC_4","NTC_6","NTC_7","NTC_8","NTC_9","NTC_11","NTC_12","NTC_13","NTC_14","NTC_15","NTC_10")

PC<-c("PC_1","PC_2","PC_8","PC_4","PC_3","PC_5","PC_6","PC_7","UR009768","UR009909","PC01")

## Ensure unique IDs within each vector
Group1 <- unique(Group1); Group2 <- unique(Group2); Group3 <- unique(Group3)
Group4 <- unique(Group4); Group5 <- unique(Group5); NTC <- unique(NTC); PC <- unique(PC)

## The group order you want everywhere (plots + stats)
group_levels <- c("Group1","Group2","Group3","Group4","Group5","NTC","PC")

## -----------------------------
## 0.1) Sample subset (union of all groups)
keep_samples <- unique(c(Group1, Group2, Group3, Group4, Group5, NTC, PC))

## -----------------------------
## 0.2) Helper: assign Group as an ordered factor (membership-based)
add_group <- function(mpse_obj) {
    sn <- rownames(colData(mpse_obj))
    grp <- rep(NA_character_, length(sn))

    grp[sn %in% Group1] <- "Group1"
    grp[sn %in% Group2] <- "Group2"
    grp[sn %in% Group3] <- "Group3"
    grp[sn %in% Group4] <- "Group4"
    grp[sn %in% Group5] <- "Group5"
    grp[sn %in% NTC]    <- "NTC"
    grp[sn %in% PC]     <- "PC"

    colData(mpse_obj)$Group <- factor(grp, levels = group_levels)

    # warn if any samples weren't assigned (helps catch typos / missing IDs)
    if (any(is.na(colData(mpse_obj)$Group))) {
        warning(
            "Unassigned samples (not found in any group list): ",
            paste(sn[is.na(colData(mpse_obj)$Group)], collapse = ", ")
        )
    }
    mpse_obj
}

## -----------------------------
## 0.3) Colors (edit to taste)
group_colors <- c(
    "Group1" = "#1f77b4",
    "Group2" = "#ff7f0e",
    "Group3" = "#2ca02c",
    "Group4" = "#d62728",
    "Group5" = "#9467bd",
    "NTC"    = "#7f7f7f",
    "PC"     = "#8c564b"
)

## =========================================================
## 1) Diversity analysis object (alpha + beta)
##    IMPORTANT: start from ps_filt (all taxa retained)
## =========================================================
ps_div <- prune_samples(keep_samples, ps_filt)
ps_div <- prune_taxa(taxa_sums(ps_div) > 0, ps_div)

mpse_div <- as.MPSE(ps_div)
mpse_div <- add_group(mpse_div)

cat("\n[mpse_div] Group counts:\n")
print(table(colData(mpse_div)$Group, useNA = "ifany"))

## =========================================================
## 2) Alpha diversity (rarefaction-based)
## =========================================================
set.seed(9242)
mpse_div %<>% mp_rrarefy()  # creates RareAbundance
mpse_div %<>% mp_cal_rarecurve(.abundance = RareAbundance, chunks = 400)

# Rarefaction curves: sample + grouped
p_rare_1 <- mpse_div %>% mp_plot_rarecurve(.rare = RareAbundanceRarecurve, .alpha = Observe)

p_rare_2 <- mpse_div %>%
    mp_plot_rarecurve(.rare = RareAbundanceRarecurve, .alpha = Observe, .group = Group) +
    scale_color_manual(values = group_colors, guide = "none") +
    scale_fill_manual(values = group_colors, guide = "none")

p_rare_3 <- mpse_div %>%
    mp_plot_rarecurve(.rare = RareAbundanceRarecurve, .alpha = "Observe",
                                        .group = Group, plot.group = TRUE) +
    scale_color_manual(values = group_colors, guide = "none") +
    scale_fill_manual(values = group_colors, guide = "none")

png("figures/rarefaction_of_samples_or_groups.png", width = 1080, height = 600)
print(p_rare_1 + p_rare_2 + p_rare_3)
dev.off()

# Alpha indices from RareAbundance
mpse_div %<>% mp_cal_alpha(.abundance = RareAbundance)

f_alpha_1 <- mpse_div %>%
    mp_plot_alpha(.group = Group, .alpha = c(Observe, Chao1, ACE, Shannon, Simpson, Pielou)) +
    scale_color_manual(values = group_colors, guide = "none") +
    scale_fill_manual(values = group_colors, guide = "none")

f_alpha_2 <- mpse_div %>%
    mp_plot_alpha(.alpha = c(Observe, Chao1, ACE, Shannon, Simpson, Pielou))

png("figures/alpha_diversity_comparison.png", width = 1400, height = 600)
print(f_alpha_1 / f_alpha_2)
dev.off()

## =========================================================
## 3) Beta diversity (Bray–Curtis on Hellinger)
##    IMPORTANT: use non-rarefied Abundance (not taxa-filtered)
## =========================================================
mpse_div %<>% mp_decostand(.abundance = Abundance)             # creates 'hellinger'
mpse_div %<>% mp_cal_dist(.abundance = hellinger, distmethod = "bray")

# Distance between samples
p_dist_1 <- mpse_div %>% mp_plot_dist(.distmethod = bray)
png("figures/distance_between_samples.png", width = 1000, height = 1000)
print(p_dist_1)
dev.off()

# Distance with group info
p_dist_2 <- mpse_div %>% mp_plot_dist(.distmethod = bray, .group = Group) +
    scale_fill_manual(values = group_colors) +
    scale_color_gradient()

png("figures/distance_between_samples_with_group_info.png", width = 1000, height = 1000)
print(p_dist_2)
dev.off()

# Compare distances between groups (Bray)
p_dist_3 <- mpse_div %>%
    mp_plot_dist(.distmethod = bray, .group = Group, group.test = TRUE, textsize = 6) +
    theme(
        axis.title.x = element_text(size = 14),
        axis.title.y = element_text(size = 14),
        axis.text.x  = element_text(size = 14),
        axis.text.y  = element_text(size = 14)
    )

png("figures/Comparison_of_Bray_Distances.png", width = 1000, height = 1000)
print(p_dist_3)
dev.off()

## PCoA + PERMANOVA (adonis2)
mpse_div %<>% mp_cal_pcoa(.abundance = hellinger, distmethod = "bray")

mpse_div %<>% mp_adonis(
    .abundance   = hellinger,
    .formula     = ~ Group,
    distmethod   = "bray",
    permutations = 9999,
    action       = "add"
)

cat("\n[PERMANOVA result]\n")
print(mpse_div %>% mp_extract_internal_attr(name = "adonis"))

## PCoA plot
p_pcoa_1 <- mpse_div %>%
    mp_plot_ord(
        .ord   = pcoa,
        .group = Group,
        .color = Group,
        .size  = 4,
        .alpha = 1,
        ellipse = TRUE,
        show.legend = TRUE
    ) +
    scale_fill_manual(values = group_colors) +
    scale_color_manual(values = group_colors) +
    theme(
        axis.text   = element_text(size = 16),
        axis.title  = element_text(size = 18),
        legend.text = element_text(size = 14),
        legend.title= element_text(size = 16)
    )

png("figures/PCoA.png", width = 1200, height = 1000)
print(p_pcoa_1)
dev.off()

pdf("figures/PCoA.pdf", width = 10, height = 8)
print(p_pcoa_1)
dev.off()

## Optional: label points
colData(mpse_div)$ShortLabel <- gsub("sample-", "", rownames(colData(mpse_div)))

p_pcoa_2 <- p_pcoa_1 +
    geom_text_repel(aes(label = ShortLabel), size = 4, max.overlaps = 100)

png("figures/PCoA_labeled.png", width = 1200, height = 1000)
print(p_pcoa_2)
dev.off()
#[PERMANOVA result]
#The object contained internal attribute: PCoA ADONIS
#Permutation test for adonis under reduced model
#Permutation: free
#Number of permutations: 9999
#
#vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)
#          Df SumOfSqs      R2      F Pr(>F)
#Model      6   11.446 0.16058 7.3971  1e-04 ***
#Residual 232   59.829 0.83942
#Total    238   71.274 1.00000
#---
#Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

## =========================================================
## 4) Composition plots object (clean taxa set for plotting)
##    IMPORTANT: start from ps_abund_rel (plotting-filtered taxa)
## =========================================================
ps_plot <- prune_samples(keep_samples, ps_abund_rel)
ps_plot <- prune_taxa(taxa_sums(ps_plot) > 0, ps_plot)

mpse_plot <- as.MPSE(ps_plot)
mpse_plot <- add_group(mpse_plot)

## Summaries for plotting (Class)
mpse_plot %<>%
    mp_cal_abundance(.abundance = Abundance) %>%               # per sample
    mp_cal_abundance(.abundance = Abundance, .group = Group)   # per group

## Class abundance barplots (top 20)
p_class_rel <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        taxa.class = Class,
        topn = 20,
        relative = TRUE
    )

p_class_abs <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        taxa.class = Class,
        topn = 20,
        relative = FALSE
    )

png("figures/relative_abundance_and_abundance_samples.png", width = 1200, height = 600)
print(p_class_rel / p_class_abs)
dev.off()

## Heatmaps (grouped)
h_rel <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        .group = Group,
        taxa.class = Class,
        relative = TRUE,
        topn = 20,
        geom = "heatmap",
        features.dist = "euclidean",
        features.hclust = "average",
        sample.dist = "bray",
        sample.hclust = "average"
    )

h_abs <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        .group = Group,
        taxa.class = Class,
        relative = FALSE,
        topn = 20,
        geom = "heatmap",
        features.dist = "euclidean",
        features.hclust = "average",
        sample.dist = "bray",
        sample.hclust = "average"
    )

png("figures/relative_abundance_and_abundance_heatmap.png", width = 1200, height = 600)
print(aplot::plot_list(gglist = list(h_rel, h_abs), tag_levels = "A"))
dev.off()

## Group-level barplots
p_group_rel <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        .group = Group,
        taxa.class = Class,
        topn = 20,
        plot.group = TRUE,
        relative = TRUE
    ) +
    scale_fill_manual(values = group_colors)

p_group_abs <- mpse_plot %>%
    mp_plot_abundance(
        .abundance = Abundance,
        .group = Group,
        taxa.class = Class,
        topn = 20,
        plot.group = TRUE,
        relative = FALSE
    ) +
    scale_fill_manual(values = group_colors)

png("figures/relative_abundance_and_abundance_groups.png", width = 1000, height = 1000)
print(p_group_rel / p_group_abs)
dev.off()

cat("\nDONE. Outputs written to ./figures/\n")

## =========================================================
## CONTINUE: Export Bray distances + pairwise PERMANOVA
## (Use mpse_div from the updated script above)
## =========================================================

suppressPackageStartupMessages({
    library(dplyr)
    library(tidyr)
    library(openxlsx)
    library(vegan)
})

## -----------------------------
## Helper: get assay matrix with rows = samples, cols = features
get_sample_by_feature <- function(mpse_obj, assay_name) {
    mat <- assay(mpse_obj, assay_name)

    # sample IDs in MPSE
    samp_ids <- rownames(colData(mpse_obj))

    # If samples are columns, transpose
    if (!is.null(colnames(mat)) && all(samp_ids %in% colnames(mat))) {
        mat <- t(mat)
    }

    # Now enforce row order to match colData
    mat <- mat[samp_ids, , drop = FALSE]
    mat
}

## -----------------------------
## 1) Recompute Bray–Curtis distance (robust extraction)
hell_mat_sf <- get_sample_by_feature(mpse_div, "hellinger")  # rows=samples, cols=features
bray_dist   <- vegdist(hell_mat_sf, method = "bray")

## sanity checks
stopifnot(!any(is.na(as.matrix(bray_dist))))
stopifnot(!any(as.matrix(bray_dist) < 0, na.rm = TRUE))

## -----------------------------
## 2) Export all pairwise Bray distances to Excel
bray_mat <- as.matrix(bray_dist)
samples  <- rownames(bray_mat)

bray_df <- as.data.frame(as.table(bray_mat)) %>%
    rename(Sample1 = Var1, Sample2 = Var2, BrayDistance = Freq) %>%
    filter(Sample1 < Sample2) %>%
    arrange(Sample1, Sample2)

write.xlsx(bray_df, file = "figures/Bray_Curtis_Distances.xlsx")

## -----------------------------
## 3) Pairwise PERMANOVA (post-hoc) using vegan::adonis2
meta2 <- as.data.frame(colData(mpse_div))
meta2 <- meta2[rownames(hell_mat_sf), , drop = FALSE]
meta2$Group <- droplevels(meta2$Group)

groups <- levels(meta2$Group)

res_list <- list()
k <- 1

for (i in 1:(length(groups) - 1)) {
    for (j in (i + 1):length(groups)) {

        g1 <- groups[i]
        g2 <- groups[j]

        idx <- meta2$Group %in% c(g1, g2)
        sub_meta <- meta2[idx, , drop = FALSE]

        sub_dist <- as.dist(as.matrix(bray_dist)[idx, idx])

        ad <- adonis2(sub_dist ~ Group, data = sub_meta, permutations = 9999)

        res_list[[k]] <- data.frame(
            group1 = g1,
            group2 = g2,
            F      = ad$F[1],
            R2     = ad$R2[1],
            p      = ad$`Pr(>F)`[1]
        )
        k <- k + 1
    }
}

pair_res <- do.call(rbind, res_list)
pair_res$p_adj_BH         <- p.adjust(pair_res$p, method = "BH")
pair_res$p_adj_Bonferroni <- p.adjust(pair_res$p, method = "bonferroni")

write.csv(pair_res, "figures/Bray_pairwise_PERMANOVA.csv", row.names = FALSE)

cat("\nPairwise PERMANOVA written to: figures/Bray_pairwise_PERMANOVA.csv\n")
cat("Bray distance table written to: figures/Bray_Curtis_Distances.xlsx\n")

## =========================================================
## OPTIONAL: PCoA plot where point size = Shannon and alpha = Observe
## (requires mpse_div already has Shannon/Observe from mp_cal_alpha)
## =========================================================

p_pcoa_sizealpha <- mpse_div %>%
    mp_plot_ord(
        .ord   = pcoa,
        .group = Group,
        .color = Group,
        .size  = Shannon,
        .alpha = Observe,
        ellipse = TRUE,
        show.legend = TRUE
    ) +
    scale_fill_manual(values = group_colors) +
    scale_color_manual(values = group_colors) +
    scale_size_continuous(range = c(2, 6)) +
    theme(
        axis.text   = element_text(size = 16),
        axis.title  = element_text(size = 18),
        legend.text = element_text(size = 14),
        legend.title= element_text(size = 16)
    )

png("figures/PCoA_sizealpha.png", width = 1200, height = 1000)
print(p_pcoa_sizealpha)
dev.off()

pdf("figures/PCoA_sizealpha.pdf", width = 10, height = 8)
print(p_pcoa_sizealpha)
dev.off()

## =========================================================
## Ensure all three ordination outputs exist:
##   - PCoA  : basic (color/group)
##   - PCoA2 : size = Shannon, alpha = Observe
##   - PCoA3 : same as PCoA2 + sample labels
##
## Assumes you already have:
##   - mpse_div with: pcoa, Group, Shannon, Observe
##   - group_colors defined
## =========================================================

p1 <- mpse_div %>%
    mp_plot_ord(
        .ord   = pcoa,
        .group = Group,
        .color = Group,
        .size  = 4,
        .alpha = 1,
        ellipse = TRUE,
        show.legend = FALSE
    ) +
    scale_fill_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 1.6,
            keyheight = 1.6,
            label.theme = element_text(size = 16)
        )
    ) +
    scale_color_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 1.6,
            keyheight = 1.6,
            label.theme = element_text(size = 16)
        )
    ) +
    theme(
        axis.text   = element_text(size = 20),
        axis.title  = element_text(size = 22),
        legend.text = element_text(size = 20),
        legend.title= element_text(size = 22),
        plot.title  = element_text(size = 24, face = "bold"),
        plot.subtitle = element_text(size = 20)
    )

png("PCoA.png", width = 1200, height = 1000)
p1
dev.off()
pdf("PCoA.pdf")
p1
dev.off()

p2 <- mpse_div %>%
    mp_plot_ord(
        .ord   = pcoa,
        .group = Group,
        .color = Group,
        .size  = Shannon,
        .alpha = Observe,
        ellipse = TRUE,
        show.legend = FALSE
    ) +
    scale_fill_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    scale_color_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    scale_size_continuous(
        range = c(2, 6),
        guide = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    theme(
        axis.text   = element_text(size = 20),
        axis.title  = element_text(size = 22),
        legend.text = element_text(size = 20),
        legend.title= element_text(size = 22),
        plot.title  = element_text(size = 24, face = "bold"),
        plot.subtitle = element_text(size = 20)
    )

png("PCoA2.png", width = 1200, height = 1000)
p2
dev.off()
pdf("PCoA2.pdf")
p2
dev.off()

library(ggrepel)
colData(mpse_div)$ShortLabel <- gsub("sample-", "", mpse_div@colData@rownames)

p3 <- mpse_div %>%
    mp_plot_ord(
        .ord   = pcoa,
        .group = Group,
        .color = Group,
        .size  = Shannon,
        .alpha = Observe,
        ellipse = TRUE,
        show.legend = FALSE
    ) +
    geom_text_repel(aes(label = ShortLabel), size = 5, max.overlaps = 100) +
    scale_fill_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    scale_color_manual(
        values = group_colors,
        guide  = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    scale_size_continuous(
        range = c(2, 6),
        guide = guide_legend(
            keywidth = 0.6,
            keyheight = 0.6,
            label.theme = element_text(size = 16)
        )
    ) +
    theme(
        axis.text   = element_text(size = 20),
        axis.title  = element_text(size = 22),
        legend.text = element_text(size = 20),
        legend.title= element_text(size = 22),
        plot.title  = element_text(size = 24, face = "bold"),
        plot.subtitle = element_text(size = 20)
    )

png("PCoA3.png", width = 1200, height = 1000)
p3
dev.off()
svg("PCoA3.svg", width = 12, height = 10)
p3
dev.off()
pdf("PCoA3.pdf")
p3
dev.off()

Phyloseq.Rmd for Data_Childrensclinic_16S_2025

Leave a reply 
author: ""
date: '`r format(Sys.time(), "%d %m %Y")`'
header-includes:
     - \usepackage{color, fancyvrb}
output:
    rmdformats::readthedown:
        highlight: kate
        number_sections : yes
    pdf_document:
        toc: yes
        toc_depth: 2
        number_sections : yes
---

```{r load-packages, include=FALSE}

#install.packages(c("picante", "rmdformats"))
#mamba install -c conda-forge freetype libpng harfbuzz fribidi
#mamba install -c conda-forge r-systemfonts r-svglite r-kableExtra freetype fontconfig harfbuzz fribidi libpng
library(knitr)
library(rmdformats)
library(readxl)
library(dplyr)
library(kableExtra)
library(openxlsx)
library(DESeq2)
library(writexl)

options(max.print="75")
knitr::opts_chunk$set(fig.width=8,
                                            fig.height=6,
                                            eval=TRUE,
                                            cache=TRUE,
                                            echo=TRUE,
                                            prompt=FALSE,
                                            tidy=FALSE,
                                            comment=NA,
                                            message=FALSE,
                                            warning=FALSE)
opts_knit$set(width=85)
# Phyloseq R library
#* Phyloseq web site : https://joey711.github.io/phyloseq/index.html
#* See in particular tutorials for
#    - importing data: https://joey711.github.io/phyloseq/import-data.html
#    - heat maps: https://joey711.github.io/phyloseq/plot_heatmap-examples.html
#rmarkdown::render('Phyloseq.Rmd',output_file='Phyloseq.html')
#options(max.print = 1e6)
```

# Data

Import raw data and assign sample key:

```{r, echo=FALSE, warning=FALSE}
#extend qiime2_metadata_for_qza_to_phyloseq.tsv with Diet and Flora
#setwd("~/DATA/Data_Laura_16S_2/core_diversity_e4753")
#map_corrected <- read.csv("qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1)
#knitr::kable(map_corrected) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
```

# Prerequisites to be installed

* R : https://pbil.univ-lyon1.fr/CRAN/
* R studio : https://www.rstudio.com/products/rstudio/download/#download

```R
install.packages("dplyr")     # To manipulate dataframes
install.packages("readxl")    # To read Excel files into R
install.packages("ggplot2")   # for high quality graphics
install.packages("heatmaply")
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
```

```{r libraries, echo=TRUE, message=FALSE}
#mamba install -c conda-forge r-ggplot2 r-vegan r-data.table
#BiocManager::install("microbiome")
#install.packages("ggpubr")
#install.packages("heatmaply")
library("readxl") # necessary to import the data from Excel file
library("ggplot2") # graphics
library("picante")
library("microbiome") # data analysis and visualisation
library("phyloseq") # also the basis of data object. Data analysis and visualisation
library("ggpubr") # publication quality figures, based on ggplot2
library("dplyr") # data handling, filter and reformat data frames
library("RColorBrewer") # nice color options
library("heatmaply")
library(vegan)
library(gplots)
#install.packages("openxlsx")
library(openxlsx)
```

# Read the data and create phyloseq objects

Three tables are needed

* OTU
* Taxonomy
* Samples

## Create analysis-specific phyloseq objects

We maintain **one filtered “base” phyloseq object** and then derive **analysis-specific** objects from it.
This avoids accidental overwriting and ensures each analysis uses the appropriate data scale (counts vs. relative abundance vs. rarefied counts).

- **`ps_raw`** → Raw imported phyloseq object (**integer counts**; import stage only)
- **`ps_base`** → `ps_raw` with **taxonomy + sample metadata** properly aligned (the clean master object before any filtering)
- **`ps_pruned`** → Optional **sample subset** of `ps_base` (e.g., drop unwanted samples by ID/pattern); still **integer counts**
- **`ps_filt`** → The shared filtered backbone: **low-depth samples removed** + taxa with **zero total counts dropped**; remains **integer counts**

```{r, echo=FALSE, warning=FALSE}

        library(tidyr)

        # For QIIME1
        #ps.ng.tax <- import_biom("./exported_table/feature-table.biom", "./exported-tree/tree.nwk")

        # For QIIME2
        #install.packages("remotes")
        #remotes::install_github("jbisanz/qiime2R")
        #"core_metrics_results/rarefied_table.qza", rarefying performed in the code, therefore import the raw table.
        library(qiime2R)
        ps_raw <- qza_to_phyloseq(
            features =  "dada2_tests/test_59_f235_r245/table.qza",
            tree = "rooted-tree.qza",
            metadata = "qiime2_metadata_for_qza_to_phyloseq.tsv"
        )

        # Refresh/ensure sample_data (optional but keeps things explicit)
        sample_df <- read.csv("./qiime2_metadata_for_qza_to_phyloseq.tsv", sep="\t", row.names=1, check.names=FALSE)
        SAM <- sample_data(sample_df, errorIfNULL = TRUE)

        # Add taxonomy table (exported from QIIME2)
        taxonomy <- read.delim("./exported-taxonomy/taxonomy.tsv", sep="\t", header=TRUE)

        # Separate taxonomy string into separate ranks
        taxonomy_df <- taxonomy %>% separate(Taxon, into = c("Domain","Phylum","Class","Order","Family","Genus","Species"), sep = ";", fill = "right", extra = "drop")
        # Use Feature.ID as rownames
        rownames(taxonomy_df) <- taxonomy_df$Feature.ID
        taxonomy_df <- taxonomy_df[, -c(1, ncol(taxonomy_df))]  # Drop Feature.ID and Confidence
        # Create tax_table
        tax_table_final <- phyloseq::tax_table(as.matrix(taxonomy_df))

        # Base object: raw integer counts + metadata + taxonomy
        ps_base <- merge_phyloseq(ps_raw, SAM, tax_table_final)
        print(ps_base)

        #colnames(phyloseq::tax_table(ps_base)) <- c("Domain","Phylum","Class","Order","Family","Genus","Species")
        saveRDS(ps_base, "./ps_base.rds")
```

Visualize data
```{r, echo=TRUE, warning=FALSE}
# Inspect the base object (raw integer counts)
sample_names(ps_base)
rank_names(ps_base)
sample_variables(ps_base)

# Optional: prune to a naming pattern (avoids hard-coding long sample lists)
#samples_keep <- sample_names(ps_base)
#samples_keep <- samples_keep[grepl("^sample-[A-H]", samples_keep)]
samples_keep <- c("O23092004","O24010402","O23083101","A23080101","PC_8","O23092702","O24010401","O23092001","O23082402","U25011701","O23120702","O23121301","O23112304","U24111801","PC01","A24080201","A23060602","A23051102","UR009768","O24031305","O23090801","UR009909","U24121801","O23120103","U23090801","O23121501","O23110901","A23051103","O24013102","O24011801","O23091403","O23102704","O24020903","A24030402","O23100401","U24101801","O24011105","O24010302","O23121502","O23092005","O24021402","O23102602","NTC_3","O23111502","PC_7","A24071701","O23111501","O24011005","A23112001","U24080201","O24010404","O23112205","O23092803","NTC_6","NTC_8","O24011001","O24010301","O24013104","O24020103","O24011201","O23102601","NTC_2","A23112002","O23102502","O24020901","O24021502","O24021503","O23112901","O23112303","O23112201","O23112902","O24020703","O24010403","O23092003","U23052401","O24021501","O23120701","NTC_11","O24022101","O24011202","O23110902","O23092701","O24011002","A24031201","U23052201","O24021401","O23091303","O24021601","NTC_13","O23092104","O24011102","O23092102","NTC_10","O24022302","A24072901","O24022301","O24022202","O24022901","A24062801","O24011004","O23090602","O23112204","O23100701","O24012403","O24011003","A24071901","O24020802","O24021403","O24021602","NTC_14","NTC_9","PC_1","O24011901","O24013103","O24021404","O24030601","O24020701","O24011204","O24011103","A24030401","NTC_4","O24020902","O23092201","NTC_7","U23071901","O24020904","O23110903","U25011702","U23071701","O24031304","O24030602","O23091501","O24012401","O24030603","O24020704","PC_4","O23110904","O24020804","O23100801","O24030604","O23100802","NTC_15","O24022201","O24012501","O23100706","O23090601","O23100803","O24031301","O23082303","O24010501","O24022902","O23102703","O23110203","O23092202","NTC_12","O23102701","O23082302","O23121304","NTC_16","O24020803","O23090802","O24020101","U25020701","O23121306","O23082301","O23092203","O23110302","O23120101","O24020905","PC_5","O23092802","U25022101","O23100702","PC_6","O23110301","O23081801","O24020705","O24011207","O23091302","O23083001","O23102503","O23121303","O24011206","O24011802","O23102504","O23110204","O24022102","O23120104","O23092002","O23102603","O23092101","O23100503","O23092103","O23111601","O24012402","O24013105","PC_3","O23092801","O23091301","O23100402","O23121503","O24011104","O23112206","O23100703","O23102702","O24022801","O24011203","O23091401","O23090803","O23100705","O23102604","O23091402","PC_2","O23121302","U24070401","O23092006","O23100704","O23112203","O24020702","O24020102","O23112301","O23100804","O24020805","O23121305","O23112202","O24011205","O24013101","O24020801","O23110202","O24031302","O23111602","O23102501","O23110101","O23090701","O24011101","O23091305","O23083102","O24021603","O23112302")
ps_pruned <- prune_samples(samples_keep, ps_base)

# Drop taxa absent after pruning
ps_pruned <- prune_taxa(taxa_sums(ps_pruned) > 0, ps_pruned)

# Quick sanity checks
nsamples(ps_base); ntaxa(ps_base)
nsamples(ps_pruned); ntaxa(ps_pruned)
```

Preprocessing statistics for each sample
```{r, echo=TRUE, warning=FALSE}
 denoising_stats <- read.csv("dada2_tests/test_59_f235_r245/data_stats.tsv", sep="\t")
 # Display the table
 kable(denoising_stats, caption = "Preprocessing statistics for each sample") %>%
     kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
```

In the QC filtering step, we removed 14 samples that either fell below the minimum sequencing depth (library size < 12,201 reads) or were pre-specified for exclusion via sample_ids (as defined in the previous step). The filtered object (ps_filt) therefore contains only samples meeting the depth cutoff, and taxa were re-pruned to retain only those with nonzero total abundance across the retained samples.

```{r, echo=TRUE, warning=FALSE}
# ------------------------------------------------------------
#   Filter low-depth samples (recommended for all analyses)
# ------------------------------------------------------------
min_depth <- 12201  # <-- adjust to your data / study design, keeps all!
ps_filt <- prune_samples(sample_sums(ps_pruned) >= min_depth, ps_pruned)
ps_filt <- prune_taxa(taxa_sums(ps_filt) > 0, ps_filt)
ps_filt

# Keep a depth summary for reporting / QC
depth_summary <- summary(sample_sums(ps_filt))
depth_summary
```

**Differential abundance (DESeq2)** → **`ps_deseq`**: **non-rarefied integer counts** derived from `ps_filt`, with optional **count-based** taxon prefilter
    *(default: taxa total counts ≥ 10 across all samples)*

From `ps_filt` (e.g. 5669 taxa and 239 samples), we branch into analysis-ready objects in two directions:

* Direction 1 for diversity analyses

    - **Alpha diversity**: `ps_rarefied` ✅ (common)
    - **Beta diversity**:
        - **Unweighted UniFrac / Jaccard**: `ps_rarefied` ✅ (often recommended)
        - **Bray–Curtis / ordination on abundances**: `ps_rel` or Hellinger ✅ (rarefaction optional)
        - **Aitchison (CLR)**: CLR-transformed (non-rarefied) ✅ (no rarefaction)

Rarefaction

```{r, echo=TRUE, warning=FALSE}

# RAREFACTION
set.seed(9242)  # This will help in reproducing the filtering and nomalisation.
ps_rarefied <- rarefy_even_depth(ps_filt, sample.size = 12201)

# # NORMALIZE number of reads in each sample using median sequencing depth.
# total = median(sample_sums(ps.ng.tax))
# #> total
# #[1] 42369
# standf = function(x, t=total) round(t * (x / sum(x)))
# ps.ng.tax = transform_sample_counts(ps.ng.tax, standf)
# ps_rel <- microbiome::transform(ps.ng.tax, "compositional")
#
# saveRDS(ps.ng.tax, "./ps.ng.tax.rds")
```

* Direction 2 for taxonomic composition plots

    - **Taxonomic composition** → **`ps_rel`**: **relative abundance** (compositional) computed **after sample filtering** (e.g. 5669 taxa and 239 samples)
    - **Optional cleaner composition plots** → **`ps_abund` / `ps_abund_rel`**: taxa filtered for plotting (e.g., keep taxa with **mean relative abundance > 0.1%**); (e.g. 95 taxa and 239 samples)
    `ps_abund` = **counts**, `ps_abund_rel` = **relative abundance** *(use for visualization, not DESeq2)*

For the heatmaps, we focus on the most abundant OTUs by first converting counts to relative abundances within each sample. We then filter to retain only OTUs whose mean relative abundance across all samples exceeds 0.1% (0.001). We are left with 199 OTUs which makes the reading much more easy.

```{r, echo=FALSE, warning=FALSE}
# 1) Convert to relative abundances
ps_rel <- transform_sample_counts(ps_filt, function(x) x / sum(x))

# 2) Get the logical vector of which OTUs to keep (based on relative abundance)
keep_vector <- phyloseq::filter_taxa(
    ps_rel,
    function(x) mean(x) > 0.001,
    prune = FALSE
)

# 3) Use the TRUE/FALSE vector to subset absolute abundance data
ps_abund <- prune_taxa(names(keep_vector)[keep_vector], ps_filt)

# 4) Normalize the final subset to relative abundances per sample
ps_abund_rel <- transform_sample_counts(
    ps_abund,
    function(x) x / sum(x)
)
```

# Heatmaps

```{r, echo=FALSE, warning=FALSE}
datamat_ = as.data.frame(otu_table(ps_abund))
#datamat <- datamat_[c("1","2","5","6","7",  "8","9","10","12","13","14",    "15","16","17","18","19","20",  "21","22","23","24","25","26","27","28",    "29","30","31","32",  "33","34","35","36","37","38","39","51",    "40","41","42","43","44","46",  "47","48","49","50","52","53","55")]
datamat <- datamat_[c("O23092004","O24010402","O23083101","A23080101","PC_8","O23092702","O24010401","O23092001","O23082402","U25011701","O23120702","O23121301","O23112304","U24111801","PC01","A24080201","A23060602","A23051102","UR009768","O24031305","O23090801","UR009909","U24121801","O23120103","U23090801","O23121501","O23110901","A23051103","O24013102","O24011801","O23091403","O23102704","O24020903","A24030402","O23100401","U24101801","O24011105","O24010302","O23121502","O23092005","O24021402","O23102602","NTC_3","O23111502","PC_7","A24071701","O23111501","O24011005","A23112001","U24080201","O24010404","O23112205","O23092803","NTC_6","NTC_8","O24011001","O24010301","O24013104","O24020103","O24011201","O23102601","NTC_2","A23112002","O23102502","O24020901","O24021502","O24021503","O23112901","O23112303","O23112201","O23112902","O24020703","O24010403","O23092003","U23052401","O24021501","O23120701","NTC_11","O24022101","O24011202","O23110902","O23092701","O24011002","A24031201","U23052201","O24021401","O23091303","O24021601","NTC_13","O23092104","O24011102","O23092102","NTC_10","O24022302","A24072901","O24022301","O24022202","O24022901","A24062801","O24011004","O23090602","O23112204","O23100701","O24012403","O24011003","A24071901","O24020802","O24021403","O24021602","NTC_14","NTC_9","PC_1","O24011901","O24013103","O24021404","O24030601","O24020701","O24011204","O24011103","A24030401","NTC_4","O24020902","O23092201","NTC_7","U23071901","O24020904","O23110903","U25011702","U23071701","O24031304","O24030602","O23091501","O24012401","O24030603","O24020704","PC_4","O23110904","O24020804","O23100801","O24030604","O23100802","NTC_15","O24022201","O24012501","O23100706","O23090601","O23100803","O24031301","O23082303","O24010501","O24022902","O23102703","O23110203","O23092202","NTC_12","O23102701","O23082302","O23121304","NTC_16","O24020803","O23090802","O24020101","U25020701","O23121306","O23082301","O23092203","O23110302","O23120101","O24020905","PC_5","O23092802","U25022101","O23100702","PC_6","O23110301","O23081801","O24020705","O24011207","O23091302","O23083001","O23102503","O23121303","O24011206","O24011802","O23102504","O23110204","O24022102","O23120104","O23092002","O23102603","O23092101","O23100503","O23092103","O23111601","O24012402","O24013105","PC_3","O23092801","O23091301","O23100402","O23121503","O24011104","O23112206","O23100703","O23102702","O24022801","O24011203","O23091401","O23090803","O23100705","O23102604","O23091402","PC_2","O23121302","U24070401","O23092006","O23100704","O23112203","O24020702","O24020102","O23112301","O23100804","O24020805","O23121305","O23112202","O24011205","O24013101","O24020801","O23110202","O24031302","O23111602","O23102501","O23110101","O23090701","O24011101","O23091305","O23083102","O24021603","O23112302")]
# Remove rows with zero variance
datamat <- datamat[apply(datamat, 1, var) > 0, ]
# Remove cols with zero variance
#datamat <- datamat[, apply(datamat, 2, var) > 0]

# (optional) replace with your actual column names
#colnames(datamat) <- c(
#    "A24040201",...
#  )

# ---------- 0) Sample names from datamat ----------
samplenames <- sub("^sample-", "", colnames(datamat))

# ---------- 1) Read metadata ----------
meta_path <- "qiime2_metadata.tsv"
meta <- read.delim(
    meta_path,
    sep = "\t",
    header = TRUE,
    stringsAsFactors = FALSE,
    check.names = FALSE,
    comment.char = ""
)

# ---------- 2) Identify SampleID + Group columns ----------
sample_id_col <- c("#SampleID","SampleID","sample-id","sampleid")
sample_id_col <- sample_id_col[sample_id_col %in% colnames(meta)][1]
if (is.na(sample_id_col)) sample_id_col <- colnames(meta)[1]

group_col <- c("Group","group","GROUP")
group_col <- group_col[group_col %in% colnames(meta)][1]
if (is.na(group_col)) stop("No 'Group' column found in metadata.")

# ---------- 3) Build lookup: sample -> group ----------
meta_ids <- sub("^sample-", "", meta[[sample_id_col]])
meta_groups <- trimws(as.character(meta[[group_col]]))
group_map <- setNames(meta_groups, meta_ids)

# Map datamat columns to group labels
groups <- unname(group_map[samplenames])
groups[is.na(groups)] <- "unknown"

# ---------- 4) Color mapping for YOUR labels ----------
# (Adjust colors if you prefer different ones)
color_map <- c(
    "1" = "#a6cee3",
    "2" = "#1f78b4",
    "3" = "#b2df8a",
    "4" = "#33a02c",
    "5" = "#fb9a99",
    "negative control" = "#6a3d9a",
    "positive control" = "#ff7f00",
    "unknown" = "GREY"
)

# Assign colors safely
sampleCols <- unname(color_map[groups])
sampleCols[is.na(sampleCols)] <- "GREY"
names(sampleCols) <- samplenames

# ---------- 5) Checks ----------
cat("Unique groups found in datamat:\n")
print(sort(unique(groups)))
cat("\nCounts per group:\n")
print(table(groups, useNA = "ifany"))
cat("\nFirst 10 sample colors:\n")
print(head(sampleCols, 10))

# Optional: list any samples that didn't match metadata
unmatched <- samplenames[groups == "unknown"]
if (length(unmatched) > 0) {
    cat("\nWARNING: Unmatched samples (showing up to 20):\n")
    print(head(unmatched, 20))
}
```

```{r, echo=TRUE, warning=FALSE, fig.cap="Heatmap", out.width = '100%', fig.align= "center"}
## --- 1) order columns by group (and then by sample name) ---
group_order <- c("1","2","3","4","5","negative control","positive control","unknown")
groups_fac  <- factor(groups, levels = group_order, ordered = TRUE)

col_order <- order(groups_fac, samplenames)

datamat_ord     <- datamat[, col_order, drop = FALSE]
groups_ord      <- groups[col_order]
samplenames_ord <- samplenames[col_order]
sampleCols_ord  <- sampleCols[col_order]

stopifnot(identical(colnames(datamat_ord), samplenames_ord))

## group separators
grp_counts <- table(factor(groups_ord, levels = group_order))
grp_breaks <- cumsum(as.integer(grp_counts[grp_counts > 0]))

## --- 2) cluster ROWS using the *ordered* matrix (columns don't matter, but be consistent) ---
hr   <- hclust(as.dist(1 - cor(t(datamat_ord), method = "pearson")), method = "complete")
mycl <- cutree(hr, h = max(hr$height) / 1.08)

mycol_palette <- c("YELLOW","DARKBLUE","DARKORANGE","DARKMAGENTA","DARKCYAN","DARKRED",
                                     "MAROON","DARKGREEN","LIGHTBLUE","PINK","MAGENTA","LIGHTCYAN",
                                     "LIGHTGREEN","BLUE","ORANGE","CYAN","RED","GREEN")
mycol <- mycol_palette[as.vector(mycl)]

## --- 3) plot using datamat_ord and sampleCols_ord; keep column order fixed ---
library(RColorBrewer)
heatmap_colors <- colorRampPalette(brewer.pal(9, "Blues"))(100)

png("figures/heatmap.png", width = 1800, height = 2400)
heatmap.2(
    as.matrix(datamat_ord),
    Rowv = as.dendrogram(hr),
    Colv = NA,                        # IMPORTANT: do NOT cluster columns
    dendrogram = "row",
    scale = "row",
    trace = "none",
    col = heatmap_colors,
    cexRow = 1.2,
    cexCol = 0.8,
    RowSideColors = mycol,
    ColSideColors = sampleCols_ord,   # IMPORTANT: use ordered colors
    srtCol = 85,
    labRow = row.names(datamat_ord),
    labCol = samplenames_ord,         # optional but explicit
    key = TRUE,
    margins = c(10, 15),
    lhei = c(0.7, 15),
    lwid = c(1, 8),
    colsep = grp_breaks,              # optional separators
    sepcolor = "black",
    sepwidth = c(0.02, 0.02)
)
dev.off()

knitr::include_graphics("./figures/heatmap.png")
```

\pagebreak

```{r, echo=FALSE, warning=FALSE}
    library(stringr)
#for id in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100  101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199; do
#for id in 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300; do
#for id in 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382; do
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Domain\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Phylum\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Class\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Order\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Family\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Genus\"], \"__\")[[1]][2]"
#  echo "phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"] <- str_split(phyloseq::tax_table(ps_abund_rel)[${id},\"Species\"], \"__\")[[1]][2]"
#done

phyloseq::tax_table(ps_abund_rel)[1,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[1,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[1,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[2,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[2,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[3,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[3,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[4,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[4,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[5,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[5,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[6,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[6,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[7,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[7,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[8,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[8,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[9,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[9,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[10,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[10,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[11,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[11,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[12,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[12,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[13,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[13,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[14,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[14,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[15,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[15,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[16,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[16,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[17,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[17,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[18,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[18,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[19,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[19,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[20,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[20,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[21,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[21,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[22,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[22,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[23,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[23,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[24,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[24,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[25,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[25,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[26,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[26,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[27,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[27,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[28,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[28,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[29,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[29,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[30,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[30,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[31,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[31,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[32,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[32,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[33,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[33,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[34,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[34,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[35,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[35,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[36,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[36,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[37,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[37,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[38,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[38,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[39,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[39,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[40,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[40,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[41,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[41,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[42,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[42,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[43,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[43,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[44,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[44,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[45,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[45,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[46,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[46,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[47,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[47,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[48,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[48,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[49,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[49,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[50,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[50,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[51,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[51,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[52,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[52,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[53,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[53,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[54,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[54,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[55,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[55,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[56,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[56,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[57,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[57,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[58,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[58,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[59,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[59,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[60,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[60,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[61,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[61,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[62,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[62,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[63,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[63,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[64,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[64,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[65,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[65,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[66,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[66,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[67,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[67,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[68,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[68,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[69,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[69,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[70,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[70,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[71,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[71,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[72,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[72,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[73,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[73,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[74,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[74,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[75,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[75,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[76,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[76,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[77,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[77,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[78,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[78,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[79,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[79,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[80,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[80,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[81,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[81,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[82,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[82,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[83,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[83,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[84,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[84,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[85,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[85,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[86,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[86,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[87,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[87,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[88,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[88,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[89,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[89,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[90,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[90,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[91,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[91,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[92,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[92,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[93,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[93,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[94,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[94,"Species"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Domain"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Domain"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Phylum"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Phylum"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Class"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Class"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Order"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Order"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Family"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Family"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Genus"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Genus"], "__")[[1]][2]
phyloseq::tax_table(ps_abund_rel)[95,"Species"] <- str_split(phyloseq::tax_table(ps_abund_rel)[95,"Species"], "__")[[1]][2]
```

# Taxonomic summary

## Bar plots in phylum level

```{r, fig.width=16, fig.height=8, echo=TRUE, warning=FALSE}
    sample_order <- c(
            "U24080201","U25020701","O23092004","U24101801","U25022101","O23102703","A24062801","O23112205","U23071901","A23112002","U24111801","O23110101","U24121801","O23120101","O24011202","O23090803","A23060602","A24030402","U25011701","O24011901","U23090801","O24011201","O24011003","O23092202","O23082301","O23091403","O23112901","O23092201","O24013103","O24021403","O24010402","O23092005","O23092203","O24010302","O23090701","O23091501","O23092701","O24022202","O23092802","O23090601","O23100401","O24022102","O23081801","O23092006","O23100503","O23090602","O24013104","O24020803","O24010301","O24010404","O23090802","O23092801","O24022801","O23100706","O23102602","O24021601","O24012401","O24021603","O24022901","O24021501","O23110902","O23102601","O23102704","O23100803","O23102701","O24021401","O24022101","O24030603","O23110901","O23110903","O23110301","O24022301","O23102502","O23111501","O23111602","O24020705","O24021502","O24022201","O23110202","O23090801","U23071701","U23052401","U23052201","U24070401","O24011801","O23092003","A24071901","A24072901","O24011102","O23121501","O23092104","O23092001","O23121301","O24020701","O23112201","O23100701","O23100801","O24020903","O24020901","O24020703","O23112204","O23100802","O24011205","O23092002","O24011207","O23092103","O23102501","O24011005","A24030401","O24011004","A23051102","U25011702","O24011204","O23121502","O23120702","O24011206","O24021404","O23092101","O24010403","O23112303","O23083001","O23082302","O24010401","O24022302","O24010501","O23112902","O23082303","O23083102","O24013101","O23100402","O24020801","O23120701","O23121304","O24021602","O24011802","O23121306","O23120103","O24020905","O24012403","O24013102","O24021503","O24020904","O23102504","O24013105","O24030601","O23100705","O24030604","O23111601","O24020103","O24030602","O23110302","O23102603","O24031304","O24021402","O24020101","O24012501","O24020804","O23100804","O23102503","O24022902","O24020704","O23110904","O24020102","O24012402","O23102702","O23102604","O23110204","O23110203","O23083101","O23092702","O23112304","A23051103","A24071701","A23080101","A24031201","A24080201","O24011105","O23091305","O23121302","O23092803","O23091303","O23112301","O24011203","A23112001","O24011001","O24011002","O23091302","O24020902","O23092102","O23091401","O23121503","O23091402","O24020702","O23091301","O23112206","O24011103","O23121305","O24011101","O23121303","O24011104","O23120104","O23100704","O23112302","O23112203","O23100703","O24020805","O24020802","O23112202","O24031302","O23111502","O23100702","O24031301","O24031305","O23082402","NTC_2","NTC_3","NTC_16","NTC_4","NTC_6","NTC_7","NTC_8","NTC_9","NTC_11","NTC_12","NTC_13","NTC_14","NTC_15","NTC_10","UR009768","UR009909","PC01","PC_1","PC_2","PC_8","PC_4","PC_3","PC_5","PC_6","PC_7"
    )

    # create a sample ID column in sample_data (or overwrite an existing one)
    sample_data(ps_abund_rel)$SampleID <- sample_names(ps_abund_rel)

    # set the order as a factor with the desired levels
    sample_data(ps_abund_rel)$SampleID <- factor(
        sample_data(ps_abund_rel)$SampleID,
        levels = sample_order
    )

    #aes(color="Phylum", fill="Phylum") --> aes()
    #ggplot(data=data, aes(x=Sample, y=Abundance, fill=Phylum))
    my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")

    plot_bar(ps_abund_rel, x = "SampleID", fill = "Phylum") +
        geom_bar(stat = "identity", position = "stack") +
        scale_fill_manual(values = my_colors) +
        theme(
            axis.text.x = element_text(
                angle = 85,           # 85° rotation
                hjust = 1,            # right-justified so labels are neat
                vjust = 1,
                size  = 5,
                colour = "black"
            ),
            axis.text.y = element_text(size = 7, colour = "black"),
            legend.position = "bottom"
        ) +
        guides(fill = guide_legend(nrow = 2))
```

### Aggregate samples by group and normalize read counts within each group to correct for differences in sequencing depth.

```{r, echo=TRUE, warning=FALSE}
    # merge + normalize
    ps_abund_rel_group  <- merge_samples(ps_abund_rel, "Group")
    ps_abund_rel_group_ <- transform_sample_counts(
        ps_abund_rel_group,
        function(x) x / sum(x)
    )

    # desired order on x-axis
    group_order <- c("1", "2", "3", "4", "5", "negative control", "positive control")

    plot_bar(ps_abund_rel_group_, fill = "Phylum") +
        geom_bar(stat = "identity", position = "stack") +
        scale_x_discrete(limits = group_order) +          # <-- set order here
        scale_fill_manual(values = my_colors) +
        labs(x = "Group") +   # <- change x-axis label from "Sample" to "Group"
        theme(axis.text = element_text(angle = 0, size = 10, colour="black"), axis.text.x = element_text(angle = -15),hjust = 10,vjust = 2)
```

## Bar plots in class level

```{r, fig.width=16, fig.height=8, echo=TRUE, warning=FALSE}
    my_colors <- c("darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink", "khaki2", "firebrick", "brown1", "darkorange1", "cyan1", "royalblue4", "darksalmon", "darkblue","royalblue4", "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen", "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1", "brown1", "darkorange1", "cyan1", "darkgrey")
    plot_bar(ps_abund_rel, x = "SampleID", fill = "Class") +
        geom_bar(stat = "identity", position = "stack") +
        scale_fill_manual(values = my_colors) +
        theme(
            axis.text.x = element_text(
                angle = 85,
                hjust = 1,
                vjust = 1,
                size  = 5,
                colour = "black"
            ),
            axis.text.y = element_text(size = 7, colour = "black"),
            legend.position = "bottom"
        ) +
        guides(fill = guide_legend(nrow = 3))
```

### Aggregate samples by group and normalize read counts within each group to correct for differences in sequencing depth.

```{r, echo=TRUE, warning=FALSE}
    plot_bar(ps_abund_rel_group_, fill="Class") + geom_bar(aes(), stat="identity", position="stack") + scale_x_discrete(limits = group_order) +
    scale_fill_manual(values = my_colors) + labs(x = "Group") + theme(axis.text = element_text(angle = 0, size = 10, colour="black"), axis.text.x = element_text(angle = -15),hjust = 10,vjust = 2)
```
\pagebreak

## Bar plots in order level

```{r, fig.width=16, fig.height=8, echo=TRUE, warning=FALSE}
    my_colors <- c(
        "darkblue", "darkgoldenrod1", "darkseagreen", "darkorchid",
        "darkolivegreen1", "lightskyblue", "darkgreen", "deeppink",
        "khaki2", "firebrick", "brown1", "darkorange1", "cyan1",
        "royalblue4", "darksalmon", "darkblue","royalblue4",
        "dodgerblue3", "steelblue1", "lightskyblue", "darkseagreen",
        "darkgoldenrod1", "darkseagreen", "darkorchid", "darkolivegreen1",
        "brown1", "darkorange1", "cyan1", "darkgrey"
    )

    plot_bar(ps_abund_rel, x = "SampleID", fill = "Order") +
        geom_bar(stat = "identity", position = "stack") +
        scale_fill_manual(values = my_colors) +
        theme(
            axis.text.x = element_text(
                angle = 85,
                hjust = 1,
                vjust = 1,
                size  = 5,
                colour = "black"
            ),
            axis.text.y = element_text(size = 7, colour = "black"),
            legend.position = "bottom"
        ) +
        guides(fill = guide_legend(nrow = 4))
```

### Aggregate samples by group and normalize read counts within each group to correct for differences in sequencing depth.

```{r, echo=TRUE, warning=FALSE}
    plot_bar(ps_abund_rel_group_, fill="Order") + geom_bar(aes(), stat="identity", position="stack") + scale_x_discrete(limits = group_order) +
    scale_fill_manual(values = my_colors) + labs(x = "Group") + theme(axis.text = element_text(angle = 0, size = 10, colour="black"), axis.text.x = element_text(angle = -15),hjust = 10,vjust = 2)
```
\pagebreak

## Bar plots in family level

```{r, fig.width=16, fig.height=8, echo=TRUE, warning=FALSE}
    my_colors <- c(
                    "#FF0000", "#000000", "#0000FF", "#C0C0C0", "#FFFFFF", "#FFFF00", "#00FFFF", "#FFA500", "#00FF00", "#808080", "#FF00FF", "#800080", "#FDD017", "#0000A0", "#3BB9FF", "#008000", "#800000", "#ADD8E6", "#F778A1", "#800517", "#736F6E", "#F52887", "#C11B17", "#5CB3FF", "#A52A2A", "#FF8040", "#2B60DE", "#736AFF", "#1589FF", "#98AFC7", "#8D38C9", "#307D7E", "#F6358A", "#151B54", "#6D7B8D", "#FDEEF4", "#FF0080", "#F88017", "#2554C7", "#FFF8C6", "#D4A017", "#306EFF", "#151B8D", "#9E7BFF", "#EAC117", "#E0FFFF", "#15317E", "#6C2DC7", "#FBB917", "#FCDFFF", "#15317E", "#254117", "#FAAFBE", "#357EC7"
                )
    plot_bar(ps_abund_rel, x = "SampleID", fill = "Family") +
        geom_bar(stat = "identity", position = "stack") +
        scale_fill_manual(values = my_colors) +
        theme(
            axis.text.x = element_text(
                angle = 85,
                hjust = 1,
                vjust = 1,
                size  = 5,
                colour = "black"
            ),
            axis.text.y = element_text(size = 7, colour = "black"),
            legend.position = "bottom"
        ) +
        guides(fill = guide_legend(nrow = 8))
```

### Aggregate samples by group and normalize read counts within each group to correct for differences in sequencing depth.

```{r, echo=TRUE, warning=FALSE}
    plot_bar(ps_abund_rel_group_, fill="Family") + geom_bar(aes(), stat="identity", position="stack") + scale_x_discrete(limits = group_order) +
    scale_fill_manual(values = my_colors) + labs(x = "Group") + theme(axis.text = element_text(angle = 0, size = 10, colour="black"), axis.text.x = element_text(angle = -15),hjust = 10,vjust = 2)
```
\pagebreak

```{r, fig.width=16, fig.height=8, echo=FALSE, warning=FALSE}
# !!!!NOT_USED!!!!: #Export Relative abundances of Phylum, Class, Order, and Family levels across all samples in Excel files!
library(phyloseq)
library(writexl)
library(dplyr)

# Function to check for NA or empty values in a taxonomic rank
check_taxa_names <- function(tax_table, rank) {
    tax_values <- tax_table[[rank]]
    na_count <- sum(is.na(tax_values) | tax_values == "")
    cat("Number of NA or empty values in", rank, ":", na_count, "\n")
    if (na_count > 0) {
        cat("Taxa with NA or empty", rank, ":\n")
        print(tax_values[is.na(tax_values) | tax_values == ""])
    }
}

# Function to create and save relative abundance table for a given taxonomic rank with normalization
save_taxa_abundance <- function(ps, rank, output_file) {
    # Check for NA or empty values in the taxonomy table
    tax_table_df <- as.data.frame(tax_table(ps))
    check_taxa_names(tax_table_df, rank)

    # Aggregate OTUs by taxonomic rank, removing taxa with NA at the specified rank
    ps_glom <- tax_glom(ps, taxrank = rank, NArm = TRUE)

    # Extract OTU table (relative abundances)
    otu_table <- as.data.frame(otu_table(ps_glom))

    # Normalize each column to sum to 1
    otu_table_normalized <- apply(otu_table, 2, function(x) x / sum(x))

    # Convert matrix to data frame
    otu_table_normalized <- as.data.frame(otu_table_normalized)

    # Verify column sums are approximately 1.0
    col_sums <- colSums(otu_table_normalized)
    if (any(abs(col_sums - 1) > 1e-6)) {
        warning("Column sums in ", rank, " table do not equal 1.0: ", paste(col_sums, collapse = ", "))
    } else {
        cat("Column sums for ", rank, " table are all approximately 1.0\n")
    }

    # Extract taxonomy table and get the specified rank for taxa names
    tax_table_glom <- as.data.frame(tax_table(ps_glom))
    taxa_names <- tax_table_glom[[rank]]

    # Replace NA or empty strings with "Unclassified"
    taxa_names <- ifelse(is.na(taxa_names) | taxa_names == "", paste0("Unclassified_", rank), taxa_names)

    # Ensure unique row names
    taxa_names <- make.unique(taxa_names)

    # Set row names to taxa names (for internal reference)
    rownames(otu_table_normalized) <- taxa_names

    # Add taxa names as a column
    otu_table_normalized[[rank]] <- taxa_names

    # Reorder to move rank column to the first position
    otu_table_normalized <- otu_table_normalized[, c(rank, setdiff(names(otu_table_normalized), rank))]

    # Rename sample columns by removing "sample-" prefix
    names(otu_table_normalized)[-1] <- sub("sample-", "", names(otu_table_normalized)[-1])

    # Write the data frame to Excel, including the rank column
    write_xlsx(otu_table_normalized, path = output_file)
    cat("Saved", output_file, "\n")
}

# Verify column sums of ps_abund_rel
col_sums <- colSums(otu_table(ps_abund_rel))
cat("Column sums of ps_abund_rel:\n")
summary(col_sums)

## Generate Excel files for Phylum, Class, Order, and Family levels with normalization and renamed sample names
#save_taxa_abundance(ps_abund_rel, "Phylum", "relative_abundance_phylum_old.xlsx")
#save_taxa_abundance(ps_abund_rel, "Class", "relative_abundance_class_old.xlsx")
#save_taxa_abundance(ps_abund_rel, "Order", "relative_abundance_order_old.xlsx")
#save_taxa_abundance(ps_abund_rel, "Family", "relative_abundance_family_old.xlsx")
```

```{r, fig.width=16, fig.height=8, echo=FALSE, warning=FALSE}
library(phyloseq)
library(writexl)
library(dplyr)

# Function to check for NA or empty values in a taxonomic rank
check_taxa_names <- function(tax_table, rank) {
    tax_values <- tax_table[[rank]]
    na_count <- sum(is.na(tax_values) | tax_values == "")
    cat("Number of NA or empty values in", rank, ":", na_count, "\n")
    if (na_count > 0) {
        cat("Taxa with NA or empty", rank, ":\n")
        print(tax_values[is.na(tax_values) | tax_values == ""])
    }
}

# Function to create and save relative abundance table for a given taxonomic rank with normalization
save_taxa_abundance <- function(ps, rank, output_file) {
    # Clean the taxonomy table by removing D_[level]__ prefixes
    tax_table_df <- as.data.frame(tax_table(ps))
    tax_table_df[[rank]] <- ifelse(is.na(tax_table_df[[rank]]) | tax_table_df[[rank]] == "",
                                                                 paste0("Unclassified_", rank),
                                                                 sub("^D_[0-9]+__(.+)", "\\1", tax_table_df[[rank]]))
    tax_table(ps) <- as.matrix(tax_table_df)  # Update taxonomy table with cleaned names

    # Check for NA or empty values in the taxonomy table
    check_taxa_names(tax_table_df, rank)

    # Aggregate OTUs by taxonomic rank, removing taxa with NA at the specified rank
    ps_glom <- tax_glom(ps, taxrank = rank, NArm = TRUE)

    # Extract OTU table (relative abundances)
    otu_table <- as.data.frame(otu_table(ps_glom))

    # Normalize each column to sum to 1
    otu_table_normalized <- apply(otu_table, 2, function(x) x / sum(x))

    # Convert matrix to data frame
    otu_table_normalized <- as.data.frame(otu_table_normalized)

    # Verify column sums are approximately 1.0
    col_sums <- colSums(otu_table_normalized)
    if (any(abs(col_sums - 1) > 1e-6)) {
        warning("Column sums in ", rank, " table do not equal 1.0: ", paste(col_sums, collapse = ", "))
    } else {
        cat("Column sums for ", rank, " table are all approximately 1.0\n")
    }

    # Extract taxonomy table and get the specified rank for taxa names
    tax_table_glom <- as.data.frame(tax_table(ps_glom))
    taxa_names <- tax_table_glom[[rank]]

    # Ensure unique row names
    taxa_names <- make.unique(taxa_names)

    # Set row names to taxa names (for internal reference)
    rownames(otu_table_normalized) <- taxa_names

    # Add taxa names as a column
    otu_table_normalized[[rank]] <- taxa_names

    # Reorder to move rank column to the first position
    otu_table_normalized <- otu_table_normalized[, c(rank, setdiff(names(otu_table_normalized), rank))]

    # Rename sample columns by removing "sample-" prefix
    names(otu_table_normalized)[-1] <- sub("sample-", "", names(otu_table_normalized)[-1])

    # Write the data frame to Excel, including the rank column
    write_xlsx(otu_table_normalized, path = output_file)
    cat("Saved", output_file, "\n")
}

# Verify column sums of ps_abund_rel
col_sums <- colSums(otu_table(ps_abund_rel))
cat("Column sums of ps_abund_rel:\n")
summary(col_sums)

## Generate Excel files for Phylum, Class, Order, and Family levels with normalization and renamed sample names
#save_taxa_abundance(ps_abund_rel, "Phylum", "relative_abundance_phylum.xlsx")
#save_taxa_abundance(ps_abund_rel, "Class", "relative_abundance_class.xlsx")
#save_taxa_abundance(ps_abund_rel, "Order", "relative_abundance_order.xlsx")
#save_taxa_abundance(ps_abund_rel, "Family", "relative_abundance_family.xlsx")

#Sum up the last two colums with the same row.names to a new column, export the file as csv, then delete the two rows before last, then merge them with csv2xls to a Excel-file, adapt the sheet-names.
#~/Tools/csv2xls-0.4/csv_to_xls.py relative_abundance_phylum.csv relative_abundance_order.csv relative_abundance_family.csv -d$'\t' -o relative_abundance_phylum_order_family.xls;
```

\pagebreak

# Alpha diversity
Plot Chao1 richness estimator, Observed OTUs, Shannon index, and Phylogenetic diversity.
Regroup together samples from the same group.
```{r, echo=FALSE, warning=FALSE}
# using rarefied data
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even42369.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_stool/rep_set.tre
#gunzip table_even4753.biom.gz
#alpha_diversity.py -i table_even4753.biom --metrics chao1,observed_otus,shannon,PD_whole_tree -o adiv_even.txt -t ../clustering_swab/rep_set.tre
```

```{r, echo=TRUE, warning=FALSE}
hmp.meta <- meta(ps_rarefied)
hmp.meta$sam_name <- rownames(hmp.meta)

# ---- enforce Group order (edit if you have different labels) ----
group_order <- c("1","2","3","4","5","negative control", "positive control")
hmp.meta$Group <- factor(as.character(hmp.meta$Group), levels = group_order)

# for QIIME2: Lesen der Metriken
shannon <- read.table("exported_alpha/shannon/alpha-diversity.tsv", header=TRUE, sep="\t")  #cp -r ../Data_Karoline_16S_2025/exported_alpha/ .
faith_pd <- read.table("exported_alpha/faith_pd/alpha-diversity.tsv", header=TRUE, sep="\t")
observed <- read.table("exported_alpha/observed_features/alpha-diversity.tsv", header=TRUE, sep="\t")
#chao1 <- read.table("exported_alpha/chao1/alpha-diversity.tsv", header=TRUE, sep="\t")    #TODO: Check the correctness of chao1-calculation.

# Umbenennen für Klarheit
colnames(shannon) <- c("sam_name", "shannon")
colnames(faith_pd) <- c("sam_name", "PD_whole_tree")
colnames(observed) <- c("sam_name", "observed_otus")
#colnames(chao1) <- c("sam_name", "chao1")

# Merge alles in ein DataFrame
div.df <- Reduce(function(x, y) merge(x, y, by="sam_name"),
                                    list(shannon, faith_pd, observed))

# Meta-Daten einfügen
div.df <- merge(div.df, hmp.meta, by="sam_name")

# Reformat
div.df2 <- div.df[, c("sam_name", "Group", "shannon", "observed_otus", "PD_whole_tree")]
colnames(div.df2) <- c("Sample name", "Group", "Shannon", "OTU", "Phylogenetic Diversity")
write.csv(div.df2, file="alpha_diversities.txt")
knitr::kable(div.df2) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

#https://uc-r.github.io/t_test
#We can perform the test with t.test and transform our data and we can also perform the nonparametric test with the wilcox.test function.
stat.test.Shannon <- compare_means(
 Shannon ~ Group, data = div.df2,
 method = "t.test"
)
knitr::kable(stat.test.Shannon) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

div_df_melt <- reshape2::melt(div.df2)
#head(div_df_melt)

#https://plot.ly/r/box-plots/#horizontal-boxplot
#http://www.sthda.com/english/wiki/print.php?id=177
#https://rpkgs.datanovia.com/ggpubr/reference/as_ggplot.html
#http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/82-ggplot2-easy-way-to-change-graphical-parameters/
#https://plot.ly/r/box-plots/#horizontal-boxplot
#library("gridExtra")
#par(mfrow=c(4,1))
p <- ggboxplot(div_df_melt, x = "Group", y = "value",
                            facet.by = "variable",
                            scales = "free",
                            width = 0.5,
                            fill = "gray", legend= "right")
#ggpar(p, xlab = FALSE, ylab = FALSE)
lev <- levels(factor(div_df_melt$Group)) # get the variables
#FITTING4: delete H47(1) in lev
#lev <- lev[-c(3)]
# make a pairwise list that we want to compare.
#my_stat_compare_means
#https://stackoverflow.com/questions/47839988/indicating-significance-with-ggplot2-in-a-boxplot-with-multiple-groups
L.pairs <- combn(seq_along(lev), 2, simplify = FALSE, FUN = function(i) lev[i]) #%>% filter(p.signif != "ns")
my_stat_compare_means  <- function (mapping = NULL, data = NULL, method = NULL, paired = FALSE,
        method.args = list(), ref.group = NULL, comparisons = NULL,
        hide.ns = FALSE, label.sep = ", ", label = NULL, label.x.npc = "left",
        label.y.npc = "top", label.x = NULL, label.y = NULL, tip.length = 0.03,
        symnum.args = list(), geom = "text", position = "identity",
        na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
{
        if (!is.null(comparisons)) {
                method.info <- ggpubr:::.method_info(method)
                method <- method.info$method
                method.args <- ggpubr:::.add_item(method.args, paired = paired)
                if (method == "wilcox.test")
                        method.args$exact <- FALSE
                pms <- list(...)
                size <- ifelse(is.null(pms$size), 0.3, pms$size)
                color <- ifelse(is.null(pms$color), "black", pms$color)
                map_signif_level <- FALSE
                if (is.null(label))
                        label <- "p.format"
                if (ggpubr:::.is_p.signif_in_mapping(mapping) | (label %in% "p.signif")) {
                        if (ggpubr:::.is_empty(symnum.args)) {
                                map_signif_level <- c(`****` = 1e-04, `***` = 0.001,
                                    `**` = 0.01, `*` = 0.05, ns = 1)
                        } else {
                             map_signif_level <- symnum.args
                        }
                        if (hide.ns)
                                names(map_signif_level)[5] <- " "
                }
                step_increase <- ifelse(is.null(label.y), 0.12, 0)
                ggsignif::geom_signif(comparisons = comparisons, y_position = label.y,
                        test = method, test.args = method.args, step_increase = step_increase,
                        size = size, color = color, map_signif_level = map_signif_level,
                        tip_length = tip.length, data = data)
        } else {
                mapping <- ggpubr:::.update_mapping(mapping, label)
                layer(stat = StatCompareMeans, data = data, mapping = mapping,
                        geom = geom, position = position, show.legend = show.legend,
                        inherit.aes = inherit.aes, params = list(label.x.npc = label.x.npc,
                                label.y.npc = label.y.npc, label.x = label.x,
                                label.y = label.y, label.sep = label.sep, method = method,
                                method.args = method.args, paired = paired, ref.group = ref.group,
                                symnum.args = symnum.args, hide.ns = hide.ns,
                                na.rm = na.rm, ...))
        }
}

# Rotate the x-axis labels to 45 degrees and adjust their position
p <- p + theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust=1, size=8))
p2 <- p +
stat_compare_means(
    method="t.test",
    comparisons = list(c("1", "2"), c("1", "3"), c("1", "4"), c("1", "5"), c("2", "3"), c("2", "4"), c("2", "5"), c("3", "4"), c("3", "5"), c("4", "5")),
    label = "p.signif",
    symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns"))
)
#comparisons = L.pairs,
#symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05), symbols = c("****", "***", "**", "*")),
#stat_pvalue_manual
print(p2)
#https://stackoverflow.com/questions/20500706/saving-multiple-ggplots-from-ls-into-one-and-separate-files-in-r
ggsave("./figures/alpha_diversity_Group.png", device="png", height = 10, width = 15)
ggsave("./figures/alpha_diversity_Group.svg", device="svg", height = 10, width = 15)
```

```{r, echo=FALSE, warning=FALSE, fig.cap="Alpha diversity", out.width = '100%', fig.align= "center"}
## MANUALLY selected alpha diversities unter host-env after 'cp alpha_diversities.txt selected_alpha_diversities.txt'
#knitr::include_graphics("./figures/alpha_diversity_Group.png")
#selected_alpha_diversities<-read.csv("selected_alpha_diversities.txt",sep="\t")
#knitr::kable(selected_alpha_diversities) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
```

```{r, echo=FALSE, warning=FALSE, out.width = '100%', fig.align= "center"}
#!!# Beta diversity (Bray-Curtis distance)
#!!## Group1 vs Group2

#fig.cap="Beta diversity",

#for QIIME1: file:///home/jhuang/DATA/Data_Marius_16S/core_diversity_e42369/bdiv_even42369_Group/weighted_unifrac_boxplots/Group_Stats.txt

# -- for QIIME2: MANUALLY filter permanova-pairwise.csv and save as permanova-pairwise_.csv
# #grep "Permutations" exported_beta_group/permanova-pairwise.csv > permanova-pairwise_.csv
# #grep "Group1,Group2" exported_beta_group/permanova-pairwise.csv >> permanova-pairwise_.csv
# #grep "Group3,Group4" exported_beta_group/permanova-pairwise.csv >> permanova-pairwise_.csv
# beta_diversity_group_stats<-read.csv("permanova-pairwise_.csv",sep=",")
# #beta_diversity_group_stats <- beta_diversity_group_stats[beta_diversity_group_stats$Group.1 == "Group1" & beta_diversity_group_stats$Group.2 == "Group2", ]
# #beta_diversity_group_stats <- beta_diversity_group_stats[beta_diversity_group_stats$Group.1 == "Group3" & beta_diversity_group_stats$Group.2 == "Group4", ]
# knitr::kable(beta_diversity_group_stats) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

#NOTE: Run this Phyloseq.Rmd, then run the code of MicrobiotaProcess.R to manually generate Comparison_of_Bray_Distances_Group1_vs_Group2.png and Comparison_of_Bray_Distances_Group3_vs_Group4.png, then run this Phyloseq.Rmd!

#knitr::include_graphics("./figures/Comparison_of_Bray_Distances_Group1_vs_Group2.png")

```

# Principal coordinates analysis (PCoA) based on Bray–Curtis dissimilarity

Global PERMANOVA on the weighted UniFrac distance matrix indicated a significant effect of Group on overall community composition (adonis2: R² = 0.1606, F = 7.397, p = 1×10⁻⁴; 9,999 permutations).

```{r, echo=FALSE, results='asis'}
# --- Global beta-diversity (PERMANOVA) ---
cat("```text\n")
cat(
"[PERMANOVA result]\n",
"The object contained internal attribute: PCoA ADONIS\n",
"Permutation test for adonis under reduced model\n",
"Permutation: free\n",
"Number of permutations: 9999\n\n",
"vegan::adonis2(formula = .formula, data = sampleda, permutations = permutations, method = distmethod)\n",
"          Df SumOfSqs      R2      F Pr(>F)\n",
"Model      6   11.446 0.16058 7.3971  1e-04 ***\n",
"Residual 232   59.829 0.83942\n",
"Total    238   71.274 1.00000\n",
"---\n",
"Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1\n",
sep = ""
)
cat("```\n")
```

Pairwise PERMANOVA tests were performed on Bray–Curtis distance matrices to compare bacterial community composition between all pairs of sample groups (metadata column Group). For each pairwise comparison, the distance matrix was subset to samples from the two groups only, and significance was assessed using vegan::adonis2 with 9,999 permutations. Resulting p-values were adjusted for multiple testing using both Benjamini–Hochberg (BH/FDR) and Bonferroni corrections.

```{r, echo=FALSE, warning=FALSE, out.width = '100%', fig.align= "center"}
#, and the full results were exported to figures/Bray_pairwise_PERMANOVA.csv
# --- Pairwise PERMANOVA results ---

Bray_pairwise_PERMANOVA <- read.csv("figures/Bray_pairwise_PERMANOVA.csv", sep = ",")
knitr::kable(Bray_pairwise_PERMANOVA, caption = "Pairwise PERMANOVA results (distance-based community differences among Group levels).") %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

# --- Ordination figures ---

#knitr::include_graphics("./PCoA.png")
knitr::include_graphics("./PCoA2.png")
knitr::include_graphics("./PCoA3.png")
```

# Differential abundance analysis

Differential abundance analysis aims to find the differences in the abundance of each taxa between two groups of samples, assigning a significance value to each comparison.

```{r, echo=FALSE, warning=FALSE}
# ------------------------------------------------------------
#  DESeq2: non-rarefied integer counts + optional taxon prefilter
# ------------------------------------------------------------
ps_deseq <- ps_filt

Group1<-c("U24080201","U25020701","O23092004","U24101801","U25022101","O23102703","A24062801","O23112205","U23071901","A23112002","U24111801","O23110101","U24121801","O23120101","O24011202","O23090803","A23060602","A24030402","U25011701","O24011901","U23090801","O24011201","O24011003","O23092202","O23082301","O23091403","O23112901","O23092201","O24013103","O24021403","O24010402","O23092005","O23092203","O24010302","O23090701","O23091501","O23092701","O24022202","O23092802","O23090601","O23100401","O24022102","O23081801","O23092006","O23100503","O23090602","O24013104","O24020803","O24010301","O24010404","O23090802","O23092801","O24022801","O23100706","O23102602","O24021601","O24012401","O24021603","O24022901","O24021501","O23110902","O23102601","O23102704","O23100803","O23102701","O24021401","O24022101","O24030603","O23110901","O23110903","O23110301","O24022301","O23102502","O23111501","O23111602","O24020705","O24021502","O24022201","O23110202","O23090801")
Group2<-c("U23071701","U23052401","U23052201","U24070401","O24011801","O23092003","A24071901","A24072901","O24011102","O23121501","O23092104","O23092001","O23121301","O24020701","O23112201","O23100701","O23100801","O24020903","O24020901","O24020703","O23112204")
Group3<-c("O23100802","O24011205","O23092002","O24011207","O23092103","O23102501","O24011005","A24030401","O24011004","A23051102","U25011702","O24011204","O23121502","O23120702","O24011206","O24021404","O23092101","O24010403","O23112303","O23083001","O23082302","O24010401","O24022302","O24010501","O23112902","O23082303","O23083102","O24013101","O23100402","O24020801","O23120701","O23121304","O24021602","O24011802","O23121306","O23120103","O24020905","O24012403","O24013102","O24021503","O24020904","O23102504","O24013105","O24030601","O23100705","O24030604","O23111601","O24020103","O24030602","O23110302","O23102603","O24031304","O24021402","O24020101","O24012501","O24020804","O23100804","O23102503","O24022902","O24020704","O23110904","O24020102","O24012402","O23102702","O23102604","O23110204","O23110203","O23083101","O23092702")
Group4<-c("O23112304","A23051103","A24071701","A23080101","A24031201","A24080201","O24011105","O23091305","O23121302","O23092803")
Group5<-c("O23091303","O23112301","O24011203","A23112001","O24011001","O24011002","O23091302","O24020902","O23092102","O23091401","O23121503","O23091402","O24020702","O23091301","O23112206","O24011103","O23121305","O24011101","O23121303","O24011104","O23120104","O23100704","O23112302","O23112203","O23100703","O24020805","O24020802","O23112202","O24031302","O23111502","O23100702","O24031301","O24031305","O23082402")
NTC<-c("NTC_2","NTC_3","NTC_16","NTC_4","NTC_6","NTC_7","NTC_8","NTC_9","NTC_11","NTC_12","NTC_13","NTC_14","NTC_15","NTC_10")
PC<-c("PC_1","PC_2","PC_8","PC_4","PC_3","PC_5","PC_6","PC_7","UR009768","UR009909","PC01")
```

## Group 1 vs Group 2

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group1,Group2)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "2")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group1_vs_Group2"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 1 vs Group 3

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group1,Group3)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "3")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group1_vs_Group3"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 1 vs Group 4

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group1,Group4)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "4")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group1_vs_Group4"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 1 vs Group 5

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group1,Group5)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "5")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group1_vs_Group5"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 2 vs Group 3

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group2,Group3)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "3")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group2_vs_Group3"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 2 vs Group 4

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group2,Group4)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "4")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group2_vs_Group4"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 2 vs Group 5

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group2,Group5)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "5")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group2_vs_Group5"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 3 vs Group 4

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group3,Group4)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "4")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group3_vs_Group4"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 3 vs Group 5

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group3,Group5)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "5")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group3_vs_Group5"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

## Group 4 vs Group 5

```{r, echo=TRUE, warning=FALSE}
ps_deseq_sel <- data.table::copy(ps_deseq)
otu_table(ps_deseq_sel) <- otu_table(ps_deseq)[,c(Group4,Group5)]
diagdds = phyloseq_to_deseq2(ps_deseq_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "5")
diagdds <- DESeq(
    diagdds,
    test   = "Wald",
    fitType = "parametric",
    sfType  = "poscounts"  # <- important
)
resultsNames(diagdds)

res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(phyloseq::tax_table(ps_deseq_sel)[rownames(sigtab), ], "matrix"))
# file base name
fname <- "DEGs_Group4_vs_Group5"
write.xlsx(sigtab, file = paste0(fname, ".xlsx"), rowNames = TRUE)

kable(sigtab) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

library("ggplot2")
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
        scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$log2FoldChange, sigtab$Order, function(x) max(x))
x = sort(x)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
x = tapply(sigtab$log2FoldChange, sigtab$Family, function(x) max(x))
x = sort(x)
sigtab$Family = factor(as.character(sigtab$Family), levels=names(x))

#ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
# build the plot
p <- ggplot(sigtab, aes(x = log2FoldChange, y = Family, color = Order)) +
    geom_point(aes(size = padj)) +
    scale_size_continuous(name = "padj", range = c(8, 4)) +
    theme_bw() +
    theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust = 0.5))
# SVG (svglite gives crisp text)
if (!requireNamespace("svglite", quietly = TRUE)) install.packages("svglite")
ggplot2::ggsave(paste0(fname, ".svg"), plot = p, device = svglite::svglite,
                                width = 8, height = 6, units = "in", dpi = 300)
# PNG
ggplot2::ggsave(paste0(fname, ".png"), plot = p, device = "png",
                                width = 8, height = 6, units = "in", dpi = 300)
knitr::include_graphics(paste0(fname, ".png"))
```

Main workflow using QIIME2 for Data_Childrensclinic_16S_2025

Leave a reply

  1. Install and test qiime2-docker

    #Cannot run under QIIME1, switch to QIIME2: pick_open_reference_otus.py -r/home/jhuang/REFs/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fna -i test.fna -o clustering_test/ -p clustering_params.txt --parallel --verbose

docker pull quay.io/qiime2/core:2023.9

docker run -it --rm \
-v /mnt/md1/DATA/Data_Childrensclinic_16S_2025:/data \
-v /home/jhuang/REFs:/home/jhuang/REFs \
quay.io/qiime2/core:2023.9 bash
cd /data

  2. Import the fastq-files to paired-end-demux.qza

    #https://docs.qiime2.org/2018.8/tutorials/importing/

#Moving the following fastq.gz to raw_data_NOT_USED:
643805249,Kinderklinik Lauf 2 Pl.B,B04,N720-B,CGGAGCCT,S503-B,TATCCTCT,nan,nan
7909160377,Kinderkllinik Lauf 2 Pl.D,D11,N728-D,TGCAGCTA,S517-D,GCGTAAGA,nan,nan
7909188256,Kinderklinik Lauf 2 Pl.C,C10,N712-C,GTAGAGGA,S516-C,CCTAGAGT,nan,nan
O231000101,Kinderkllinik Lauf 2 Pl.D,F11,N728-D,TGCAGCTA,S520-D,AAGGCTAT,nan,nan
O231000102,Kinderkllinik Lauf 2 Pl.D,C09,N726-D,CCTAAGAC,S516-D,CCTAGAGT,nan,nan
O231000103,Kinderkllinik Lauf 2 Pl.D,C11,N728-D,TGCAGCTA,S516-D,CCTAGAGT,nan,nan
O231000902,Kinderkllinik Lauf 2 Pl.D,C12,N729-D,TCGACGTC,S516-D,CCTAGAGT,nan,nan
O23100201,Kinderklinik Lauf 2 Pl.B,D10,N727-B,CGATCAGT,S506-B,ACTGCATA,nan,nan
O23100805,Kinderklinik Lauf 2 Pl.B,F10,N727-B,CGATCAGT,S508-B,CTAAGCCT,nan,nan
O23100901,Kinderkllinik Lauf 2 Pl.D,F08,N724-D,ACTGAGCG,S520-D,AAGGCTAT,nan,nan
O23100903,Kinderkllinik Lauf 2 Pl.D,B08,N724-D,ACTGAGCG,S515-D,TTCTAGCT,nan,nan
O23100904,Kinderkllinik Lauf 2 Pl.D,C08,N724-D,ACTGAGCG,S516-D,CCTAGAGT,nan,nan
O23100905,Kinderkllinik Lauf 2 Pl.D,D10,N727-D,CGATCAGT,S517-D,GCGTAAGA,nan,nan
O23111503,Kinderkllinik Lauf 2 Pl.D,A12,N729-D,TCGACGTC,S513-D,TCGACTAG,nan,nan
O23120902,Kinderklinik Lauf 2 Pl.C,C03,N703-C,AGGCAGAA,S516-C,CCTAGAGT,nan,nan
O24022002,Kinderklinik Lauf 2 Pl.C,H12,N715-C,ATCTCAGG,S522-C,TTATGCGA,nan,nan
U23071801,Kinderklinik Lauf 2 Pl.B,B02,N718-B,GGAGCTAC,S503-B,TATCCTCT,nan,nan

rename -n 's/^([A-Z]\d+)_S\d+_L\d+_R([12])_001\.fastq\.gz$/$1_R$2.fastq.gz/' *.fastq.gz
rename 's/^([A-Z]\d+)_S\d+_L\d+_R([12])_001\.fastq\.gz$/$1_R$2.fastq.gz/' *.fastq.gz

#for file in *.fastq.gz; do echo "mv $file $(echo $file | cut -d'_' -f1 | cut -d'-' -f1-1)_$(echo $file | cut -d'_' -f4).fastq.gz"; done
for file in *.fastq.gz; do echo "mv $file $(echo $file | cut -d'_' -f1)_$(echo $file | cut -d'_' -f4).fastq.gz"; done
#MANUALLY correct several filename errors and performing in the generated commands above
#MANUALLY correct several filename errors and performing in the generated commands below

NTC_2
NTC_3
NTC_4
NTC_5
NTC_6
NTC_7
NTC_8
NTC_9
NTC_10
NTC_11
NTC_12
NTC_13
NTC_14
NTC_15
NTC_16

mv NTC-1_R1.fastq.gz NTC_1_R1.fastq.gz
mv NTC-1_R2.fastq.gz NTC_1_R2.fastq.gz
mv NTC-2_R1.fastq.gz NTC_2_R1.fastq.gz
mv NTC-2_R2.fastq.gz NTC_2_R2.fastq.gz
mv NTC-3_R1.fastq.gz NTC_3_R1.fastq.gz
mv NTC-3_R2.fastq.gz NTC_3_R2.fastq.gz
mv NTC-4_R1.fastq.gz NTC_4_R1.fastq.gz
mv NTC-4_R2.fastq.gz NTC_4_R2.fastq.gz
mv NTC-5_R1.fastq.gz NTC_5_R1.fastq.gz
mv NTC-5_R2.fastq.gz NTC_5_R2.fastq.gz
mv NTC-6_R1.fastq.gz NTC_6_R1.fastq.gz
mv NTC-6_R2.fastq.gz NTC_6_R2.fastq.gz
mv NTC-7_R1.fastq.gz NTC_7_R1.fastq.gz
mv NTC-7_R2.fastq.gz NTC_7_R2.fastq.gz
mv NTC-8_R1.fastq.gz NTC_8_R1.fastq.gz
mv NTC-8_R2.fastq.gz NTC_8_R2.fastq.gz
mv NTC-9_R1.fastq.gz NTC_9_R1.fastq.gz
mv NTC-9_R2.fastq.gz NTC_9_R2.fastq.gz
mv NTC-10_R1.fastq.gz NTC_10_R1.fastq.gz
mv NTC-10_R2.fastq.gz NTC_10_R2.fastq.gz
mv NTC-11_R1.fastq.gz NTC_11_R1.fastq.gz
mv NTC-11_R2.fastq.gz NTC_11_R2.fastq.gz
mv NTC-12_R1.fastq.gz NTC_12_R1.fastq.gz
mv NTC-12_R2.fastq.gz NTC_12_R2.fastq.gz
mv NTC-13_R1.fastq.gz NTC_13_R1.fastq.gz
mv NTC-13_R2.fastq.gz NTC_13_R2.fastq.gz
mv NTC-14_R1.fastq.gz NTC_14_R1.fastq.gz
mv NTC-14_R2.fastq.gz NTC_14_R2.fastq.gz
mv NTC-15_R1.fastq.gz NTC_15_R1.fastq.gz
mv NTC-15_R2.fastq.gz NTC_15_R2.fastq.gz
mv NTC-16_R1.fastq.gz NTC_16_R1.fastq.gz
mv NTC-16_R2.fastq.gz NTC_16_R2.fastq.gz

PC_1
PC_2
PC_3
PC_4
PC_5
PC_6
PC_7
PC_8

mv PC-1_R1.fastq.gz PC_1_R1.fastq.gz
mv PC-1_R2.fastq.gz PC_1_R2.fastq.gz
mv PC-2_R1.fastq.gz PC_2_R1.fastq.gz
mv PC-2_R2.fastq.gz PC_2_R2.fastq.gz
mv PC-3_R1.fastq.gz PC_3_R1.fastq.gz
mv PC-3_R2.fastq.gz PC_3_R2.fastq.gz
mv PC-4_R1.fastq.gz PC_4_R1.fastq.gz
mv PC-4_R2.fastq.gz PC_4_R2.fastq.gz
mv PC-5_R1.fastq.gz PC_5_R1.fastq.gz
mv PC-5_R2.fastq.gz PC_5_R2.fastq.gz
mv PC-6_R1.fastq.gz PC_6_R1.fastq.gz
mv PC-6_R2.fastq.gz PC_6_R2.fastq.gz
mv PC-7_R1.fastq.gz PC_7_R1.fastq.gz
mv PC-7_R2.fastq.gz PC_7_R2.fastq.gz
mv PC-8_R1.fastq.gz PC_8_R1.fastq.gz
mv PC-8_R2.fastq.gz PC_8_R2.fastq.gz

#MOVE the used fastq.gz to the directory raw_data
#PREPARE the conf-file --> "-rw-rw-r-- 1 jhuang jhuang 9,3K Nov 20 12:22  pe-33-manifest"
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path pe-33-manifest --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33
#--> "-rw-r--r-- 1 root   root   3,5G Nov 20 12:24  paired-end-demux.qza"

qiime demux summarize \
--i-data paired-end-demux.qza \
--o-visualization demux_pe.qzv
#--> "-rw-r--r-- 1 root   root   320K Nov 20 12:34  demux_pe.qzv"

#qiime tools view demux_pe.qzv --> Error: Visualization viewing is currently not supported in headless environments. You can view Visualizations (and Artifacts) at https://view.qiime2.org, or move the Visualization to an environment with a display and view it with `qiime tools view`.
#Open demux_pe.gzv on https://view.qiime2.org

  3. Optimizing the parameters trunc-len-f and trunc-len-r and denoising with DADA2: optimized parameters is f240_r240

    #Your amplicon (V3–V4 region) is ~464 bp, so you need ≥20–30 bp overlap
#464-38=426; 440 is the longst +12 nt for overlapping=we need 452 nt!

#Optimize the parameters --p-trunc-len-f and --p-trunc-len-r
(qiime2-amplicon-2023.9) root@4379fea45cf7:/data# ./dada2_batch_test.sh

        #!/bin/bash

        # Set your base inputs
        INPUT=paired-end-demux.qza
        TRIM_LEFT_F=17
        TRIM_LEFT_R=21

        # Output base
        OUTPUT_DIR=dada2_tests
        mkdir -p $OUTPUT_DIR

        # Loop over trunc-len-f and trunc-len-r combinations
        # Forward: from 220 to 260
        # Reverse: from 210 to 260
        #225 220 215
        i=1
        for f in 260 255 250 245 240 235 230 225 220; do
                for r in 260 255 250 245 240 235 230 225 220 215 210; do
                OUT=test_${i}_f${f}_r${r}
                echo "Running: $OUT"
                mkdir -p $OUTPUT_DIR/$OUT

                qiime dada2 denoise-paired \
                --i-demultiplexed-seqs $INPUT \
                --p-trim-left-f $TRIM_LEFT_F \
                --p-trim-left-r $TRIM_LEFT_R \
                --p-max-ee-f 3 --p-max-ee-r 5 \
                --p-trunc-len-f $f \
                --p-trunc-len-r $r \
                --p-n-threads 32 \
                --o-table $OUTPUT_DIR/$OUT/table.qza \
                --o-representative-sequences $OUTPUT_DIR/$OUT/rep-seqs.qza \
                --o-denoising-stats $OUTPUT_DIR/$OUT/denoising-stats.qza \
                --verbose > $OUTPUT_DIR/$OUT/log.txt 2>&1

                ((i++))
                done
        done

for f in dada2_tests2/test_*/denoising-stats.qza; do
qiime metadata tabulate \
    --m-input-file $f \
    --o-visualization ${f%.qza}.qzv
done

#Manually convert denoising-stats.qza to denoising-stats.tsv using https://view.qiime2.org
#Downloads to jhuang@WS-2290C:~/DATA/Data_Childrensclinic_16S_2025/dada2_tests/test_59_f235_r245$ mv ~/Downloads/data_stats.tsv .
#NTC01  33463   1732    5.18    1723    1650    4.93    1589    4.75
#O23091304  54831   7477    13.64   7409    7133    13.01   7101    12.95
#NTC01  33463   1719    5.14    1711    1648    4.92    1588    4.75
#O23091304  54831   7419    13.53   7345    7068    12.89   7046    12.85

#pandaseq.out: grep ">" A1_R1.fastq.gz_merged.fasta | wc -l #8229;  grep ">" A10_R1.fastq.gz_merged.fasta | wc -l #9165

sudo chown -R jhuang:jhuang dada2_tests
cd dada2_tests
python3 rank_dada2_params.py

# Top parameter sets by % input non-chimeric (overall):
# test_69_f230_r250: f=230, r=250, %non-chimeric=81.75, median%=84.57, merged%=83.86, samples_nonchim=253/253
# * (CHOOSEN) test_59_f235_r245: f=235, r=245, %non-chimeric=81.57, median%=84.46, merged%=83.79, samples_nonchim=253/253
# test_58_f235_r250: f=235, r=250, %non-chimeric=81.49, median%=84.35, merged%=83.61, samples_nonchim=253/253
# test_49_f240_r240: f=240, r=240, %non-chimeric=81.30, median%=84.02, merged%=83.46, samples_nonchim=253/253

# test_48_f240_r245: f=240, r=245, %non-chimeric=81.21, median%=83.95, merged%=83.33, samples_nonchim=253/253
# test_47_f240_r250: f=240, r=250, %non-chimeric=81.12, median%=83.94, merged%=83.19, samples_nonchim=253/253
# test_39_f245_r235: f=245, r=235, %non-chimeric=80.84, median%=83.59, merged%=82.98, samples_nonchim=253/253
# test_38_f245_r240: f=245, r=240, %non-chimeric=80.78, median%=83.52, merged%=82.91, samples_nonchim=253/253
# test_37_f245_r245: f=245, r=245, %non-chimeric=80.72, median%=83.36, merged%=82.81, samples_nonchim=253/253
# test_36_f245_r250: f=245, r=250, %non-chimeric=80.62, median%=83.41, merged%=82.68, samples_nonchim=253/253

  4. Visualize outputs (Using pandaseq.out, since qiime2_metadata.tsv contains the pathway of pandaseq.out)

    4.1. mkdir fastqc_out fastqc -t 4 raw_data/* -o fastqc_out/ 4.2. mkdir trim_data trimmed_unpaired cd raw_data for file in O24021602_R1.fastq.gz O24021601_R1.fastq.gz O23100705_R1.fastq.gz PC_5_R1.fastq.gz O24010402_R1.fastq.gz U23090801_R1.fastq.gz O24012402_R1.fastq.gz NTC_7_R1.fastq.gz O23121301_R1.fastq.gz O24013104_R1.fastq.gz U25020701_R1.fastq.gz O23100401_R1.fastq.gz O24020901_R1.fastq.gz NTC_1_R1.fastq.gz O24020903_R1.fastq.gz O23092002_R1.fastq.gz UR009768_R1.fastq.gz O23100402_R1.fastq.gz O23091304_R1.fastq.gz O23100703_R1.fastq.gz O23110904_R1.fastq.gz O23110903_R1.fastq.gz O23121304_R1.fastq.gz O23083101_R1.fastq.gz O23100502_R1.fastq.gz O23110301_R1.fastq.gz O24020805_R1.fastq.gz A23051102_R1.fastq.gz O23102604_R1.fastq.gz A23051103_R1.fastq.gz O23102504_R1.fastq.gz O24011205_R1.fastq.gz O23111602_R1.fastq.gz O24020905_R1.fastq.gz O23090701_R1.fastq.gz O24020702_R1.fastq.gz NTC_4_R1.fastq.gz A24072901_R1.fastq.gz NTC_10_R1.fastq.gz O23100704_R1.fastq.gz NTC_8_R1.fastq.gz O24011901_R1.fastq.gz O23111501_R1.fastq.gz O23112303_R1.fastq.gz O23112902_R1.fastq.gz O24011203_R1.fastq.gz O23092006_R1.fastq.gz O24010404_R1.fastq.gz O23090803_R1.fastq.gz O23091501_R1.fastq.gz U25022101_R1.fastq.gz O23121305_R1.fastq.gz U24080201_R1.fastq.gz U24111801_R1.fastq.gz A24040201_R1.fastq.gz O23120702_R1.fastq.gz NTC_5_R1.fastq.gz O24013105_R1.fastq.gz O23100706_R1.fastq.gz O23083102_R1.fastq.gz O23091305_R1.fastq.gz PC_7_R1.fastq.gz O24011005_R1.fastq.gz PC01_R1.fastq.gz O24011004_R1.fastq.gz O23110902_R1.fastq.gz O24020904_R1.fastq.gz A24071701_R1.fastq.gz O24021501_R1.fastq.gz O23120101_R1.fastq.gz U25011702_R1.fastq.gz O23092103_R1.fastq.gz UR009909_R1.fastq.gz O23091403_R1.fastq.gz NTC_2_R1.fastq.gz PC_1_R1.fastq.gz O24013102_R1.fastq.gz O23102704_R1.fastq.gz O24010401_R1.fastq.gz O24012501_R1.fastq.gz U24121801_R1.fastq.gz O24031304_R1.fastq.gz O23090802_R1.fastq.gz NTC_12_R1.fastq.gz O23100702_R1.fastq.gz O24011202_R1.fastq.gz O23100601_R1.fastq.gz O23100802_R1.fastq.gz O24021404_R1.fastq.gz O23112301_R1.fastq.gz O24011103_R1.fastq.gz O24030601_R1.fastq.gz U23052201_R1.fastq.gz O23100803_R1.fastq.gz O23102502_R1.fastq.gz O24011206_R1.fastq.gz O23091401_R1.fastq.gz O23092001_R1.fastq.gz O24020801_R1.fastq.gz O23082302_R1.fastq.gz O23112204_R1.fastq.gz O23100701_R1.fastq.gz O23112304_R1.fastq.gz A24031201_R1.fastq.gz O24022801_R1.fastq.gz PC_3_R1.fastq.gz O24022901_R1.fastq.gz O23092005_R1.fastq.gz O23121502_R1.fastq.gz O24021401_R1.fastq.gz U25011701_R1.fastq.gz NTC01_R1.fastq.gz O23082401_R1.fastq.gz O24022202_R1.fastq.gz NTC_6_R1.fastq.gz O24031302_R1.fastq.gz NTC_15_R1.fastq.gz NTC_13_R1.fastq.gz O24022302_R1.fastq.gz O23121303_R1.fastq.gz O24021502_R1.fastq.gz O24020704_R1.fastq.gz O23092202_R1.fastq.gz A23112002_R1.fastq.gz O23092803_R1.fastq.gz O23112203_R1.fastq.gz NTC_11_R1.fastq.gz O23091302_R1.fastq.gz A24062801_R1.fastq.gz O23121302_R1.fastq.gz O23092104_R1.fastq.gz O24020802_R1.fastq.gz O24021403_R1.fastq.gz O23112201_R1.fastq.gz O23082402_R1.fastq.gz U24070401_R1.fastq.gz O24020902_R1.fastq.gz O24030602_R1.fastq.gz NTC_3_R1.fastq.gz O24011201_R1.fastq.gz O23091301_R1.fastq.gz O23112202_R1.fastq.gz O24021503_R1.fastq.gz O23102601_R1.fastq.gz O24011002_R1.fastq.gz O23121503_R1.fastq.gz O23092004_R1.fastq.gz O23091402_R1.fastq.gz O23092701_R1.fastq.gz O24031301_R1.fastq.gz O24020703_R1.fastq.gz O24013103_R1.fastq.gz A24080201_R1.fastq.gz U23071201_R1.fastq.gz U23052401_R1.fastq.gz U23071901_R1.fastq.gz O24011101_R1.fastq.gz U23091101_R1.fastq.gz O23110204_R1.fastq.gz O23102702_R1.fastq.gz O24020101_R1.fastq.gz O24012401_R1.fastq.gz O23100501_R1.fastq.gz O24020705_R1.fastq.gz A23060602_R1.fastq.gz O23102701_R1.fastq.gz O24011001_R1.fastq.gz O24022102_R1.fastq.gz O23110302_R1.fastq.gz O23100503_R1.fastq.gz O24020803_R1.fastq.gz O23110203_R1.fastq.gz A24030402_R1.fastq.gz O23092102_R1.fastq.gz O24011003_R1.fastq.gz O23121306_R1.fastq.gz O23110101_R1.fastq.gz O24020804_R1.fastq.gz O23112901_R1.fastq.gz A23072501_R1.fastq.gz O24030604_R1.fastq.gz O23112302_R1.fastq.gz O24010301_R1.fastq.gz O24021402_R1.fastq.gz O24011104_R1.fastq.gz O23102602_R1.fastq.gz O23102703_R1.fastq.gz O23091303_R1.fastq.gz O24011204_R1.fastq.gz A24071901_R1.fastq.gz O23102603_R1.fastq.gz O23082303_R1.fastq.gz O24011801_R1.fastq.gz O24030603_R1.fastq.gz O23092802_R1.fastq.gz O23090801_R1.fastq.gz A24030401_R1.fastq.gz O23083001_R1.fastq.gz A23060601_R1.fastq.gz O23092203_R1.fastq.gz NTC_14_R1.fastq.gz O23090602_R1.fastq.gz A23111301_R1.fastq.gz O23120103_R1.fastq.gz O24011105_R1.fastq.gz U23071701_R1.fastq.gz O23111601_R1.fastq.gz O24010501_R1.fastq.gz O23110202_R1.fastq.gz O23121501_R1.fastq.gz O24010302_R1.fastq.gz O24011207_R1.fastq.gz O23092702_R1.fastq.gz O23112206_R1.fastq.gz PC_2_R1.fastq.gz O23102503_R1.fastq.gz O23092201_R1.fastq.gz NTC_9_R1.fastq.gz A23080101_R1.fastq.gz PC_6_R1.fastq.gz O23120701_R1.fastq.gz U24101801_R1.fastq.gz A23112001_R1.fastq.gz O23120104_R1.fastq.gz O23100804_R1.fastq.gz O24031305_R1.fastq.gz O23111502_R1.fastq.gz O24020103_R1.fastq.gz O23082301_R1.fastq.gz NTC_16_R1.fastq.gz PC_8_R1.fastq.gz O24022101_R1.fastq.gz O24020102_R1.fastq.gz O23081801_R1.fastq.gz O24022902_R1.fastq.gz O23112205_R1.fastq.gz O24021603_R1.fastq.gz O23102501_R1.fastq.gz O24010403_R1.fastq.gz O24012403_R1.fastq.gz O23092003_R1.fastq.gz O24013101_R1.fastq.gz O24011802_R1.fastq.gz O24011102_R1.fastq.gz PC_4_R1.fastq.gz O23100801_R1.fastq.gz O23092101_R1.fastq.gz O24020701_R1.fastq.gz O23092801_R1.fastq.gz O24022201_R1.fastq.gz O23110901_R1.fastq.gz O23090601_R1.fastq.gz O24022301_R1.fastq.gz; do java -jar /home/jhuang/Tools/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 16 $file ${file/_R1/_R2} ../trim_data/$file ../trimmed_unpaired/$file ../trim_data/${file/_R1/_R2} ../trimmed_unpaired/${file/_R1/_R2} ILLUMINACLIP:/home/jhuang/Tools/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 AVGQUAL:20; done 2> trimmomatic_pe.log

    4.3. mkdir pandaseq.out conda activate /home/jhuang/miniconda3/envs/qiime1 for file in trim_data/*_R1.fastq.gz; do pandaseq -f ${file} -r ${file/_R1.fastq.gz/R2.fastq.gz} -l 300 -p CCTACGGGNGGCWGCAG -q GACTACHVGGGTATCTAATCC -w pandaseq.out/$(echo $file | cut -d’/’ -f2 | cut -d’‘ -f1-3)_merged.fasta >> LOG_pandaseq; done conda deactivate

    4.4. prepare qiime2_metadata.tsv

    4.5. run qiime feature-table summarize \ –i-table dada2_tests/test_59_f235_r245/table.qza \ –o-visualization table.qzv \ –m-sample-metadata-file qiime2_metadata.tsv

    #Table summary
#Metric Sample
#Number of samples  137-->96
#Number of features 3,039-->21,893
#Total frequency    1,641,484-->9,246,546
#
#Frequency per sample
#Minimum frequency  413.0-->41,764.0
#1st quartile   10,319.0-->100,017.5
#Median frequency   11,530.0-->100,017.5
#3rd quartile   13,146.0-->110,183.5
#Maximum frequency  40,022.0-->143,563.0
#Mean frequency 11,981.635036496351-->96,318.1875
#
#Frequency per feature
#Minimum frequency  1.0
#1st quartile   3.0
#Median frequency   8.0-->4.0
#3rd quartile   95.5-->14.0
#Maximum frequency  56,472.0-->983,499.0
#Mean frequency 540.1395195788089-->422.35

#qiime tools peek dada2_tests/test_59_f235_r245/table.qza
#qiime tools peek qiime2_metadata.tsv

qiime feature-table tabulate-seqs \
--i-data dada2_tests/test_59_f235_r245/rep-seqs.qza \
--o-visualization rep-seqs.qzv

qiime metadata tabulate \
--m-input-file dada2_tests/test_59_f235_r245/denoising-stats.qza \
--o-visualization denoising-stats.qzv

  5. Import reference sequences and taxonomy (SILVA 132)

    qiime tools import \
--type 'FeatureData[Sequence]' \
--input-path /home/jhuang/REFs/SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fna \
--output-path silva_132_99_otus.qza \
--input-format DNAFASTAFormat

qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path /home/jhuang/REFs/SILVA_132_QIIME_release/taxonomy/16S_only/99/consensus_taxonomy_7_levels.txt \
--output-path silva_132_99_taxonomy.qza

  6. Assign taxonomy

    qiime feature-classifier classify-consensus-vsearch \
--i-query  dada2_tests/test_59_f235_r245/rep-seqs.qza \
--i-reference-reads silva_132_99_otus.qza \
--i-reference-taxonomy silva_132_99_taxonomy.qza \
--p-perc-identity 0.97 \
--p-threads 64 \
--o-classification taxonomy.qza \
--o-search-results search-results.qza

  7. Visualize taxonomy

    qiime taxa barplot \
--i-table  dada2_tests/test_59_f235_r245/table.qza \
--i-taxonomy taxonomy.qza \
--m-metadata-file qiime2_metadata.tsv \
--o-visualization taxa-bar-plots.qzv

  8. Build phylogenetic tree

    qiime alignment mafft \
--i-sequences  dada2_tests/test_59_f235_r245/rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza

qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza

qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree unrooted-tree.qza

# (*) The rooted-tree is generated from unrooted-tree, and will be used in the next step!
qiime phylogeny midpoint-root \
--i-tree unrooted-tree.qza \
--o-rooted-tree rooted-tree.qza

  9. Core diversity analysis

    #The -e 6389 flag sets the even sampling depth (rarefaction depth) to 6,389 reads for diversity analyses.
#All samples will be rarefied to 4,753 reads.
#Samples with fewer reads are excluded.
qiime diversity core-metrics-phylogenetic \
--i-phylogeny rooted-tree.qza \
--i-table  dada2_tests/test_59_f235_r245/table.qza \
--p-sampling-depth 6389 \
--m-metadata-file qiime2_metadata.tsv \
--output-dir core_metrics_results

qiime diversity alpha \
--i-table dada2_tests/test_59_f235_r245/table.qza \
--p-metric chao1 \
--o-alpha-diversity core_metrics_results/chao1_vector.qza

qiime tools export --input-path core_metrics_results/shannon_vector.qza --output-path exported_alpha/shannon
qiime tools export --input-path core_metrics_results/faith_pd_vector.qza --output-path exported_alpha/faith_pd
qiime tools export --input-path core_metrics_results/observed_features_vector.qza --output-path exported_alpha/observed_features
qiime tools export --input-path core_metrics_results/chao1_vector.qza --output-path exported_alpha/chao1

qiime tools export \
--input-path core_metrics_results/unweighted_unifrac_distance_matrix.qza \
--output-path exported_unweighted_unifrac
qiime tools export \
--input-path core_metrics_results/weighted_unifrac_distance_matrix.qza \
--output-path exported_weighted_unifrac

qiime diversity beta-group-significance \
--i-distance-matrix core_metrics_results/weighted_unifrac_distance_matrix.qza \
--m-metadata-file qiime2_metadata.tsv \
--m-metadata-column Group \
--p-pairwise \
--p-method permanova \
--o-visualization beta_group_significance.qzv

qiime tools export \
--input-path beta_group_significance.qzv \
--output-path exported_beta_group

  10. Prepare three files feeding to Phyloseq.Rmd: table.qza (see above with ), rooted-tree.qza (see above with ), qiime2_metadata_for_qza_to_phyloseq.tsv edited from qiime2_metadata.tsv.

    # Rarefying can be performed here, or in Phyloseq.Rmd (default), therefore, we don't need this step any more.
qiime feature-table summarize \
--i-table core_metrics_results/rarefied_table.qza \
--o-visualization rarefied_table.qzv \
--m-sample-metadata-file qiime2_metadata.tsv

#Table summary
#Metric Sample
#Number of samples  136
#Number of features 2,781
#Total frequency    868,904

# In QIIME2, we need table.qza, not biom-file, therefore, we don't need this step any more.
qiime tools export \
--input-path core_metrics_results/rarefied_table.qza \
--output-path exported_rarefied_table
#--> exported_rarefied_table/feature-table.biom

biom convert \
-i exported_rarefied_table/feature-table.biom \
-o exported_rarefied_table/feature-table.tsv \
--to-tsv

#✅ Old QIIME 1 table with GenBank IDs (like EF603722.1.1487) as feature labels.
#✅ QIIME 2 table where feature IDs are hashes (like 0b438323a296b5f2ce2c8bbe3949ee8d).

# Visulaize the taxonomy.qza
qiime tools export \
--input-path taxonomy.qza \
--output-path exported-taxonomy

#Feature ID    Taxon                               Confidence
#0b4383...     k__Bacteria; p__Proteobacteria...   0.98
#dfa833...     k__Bacteria; p__Firmicutes...       0.87
#...

# ---- I used the following to generate two file for feeding in the Phyloseq.Rmd ----

#-1- exported_table/feature-table.biom corresesponds to table_even6389.biom in QIIME1, but in QIIME2, we don't need biom-file, instead of table.qza.

qiime tools export \
--input-path  dada2_tests/test_59_f235_r245/table.qza \
--output-path exported_table
#--> exported_table/feature-table.biom

#-2- exported-tree/tree.nwk corresesponds to rep_set.tre in QIIME1

qiime tools export \
--input-path rooted-tree.qza \
--output-path exported-tree
#--> exported-tree/tree.nwk

# END

# ---- The code in Phyloseq.Rmd ----

#install.packages("remotes")
#remotes::install_github("jbisanz/qiime2R")
#"core_metrics_results/rarefied_table.qza", rarefying performed in the code, therefore import the raw table.
library(qiime2R)
ps.ng.tax <- qza_to_phyloseq(
    features =  "dada2_tests/test_59_f235_r245/table.qza",
    tree = "rooted-tree.qza",
    metadata = "qiime2_metadata_for_qza_to_phyloseq.tsv"
)
# or
#biom convert \
#      -i ./exported_table/feature-table.biom \
#      -o ./exported_table/feature-table-v1.biom \
#      --to-json
#ps.ng.tax <- import_biom("./exported_table/feature-table-v1.biom", treefilename="./exported-tree/tree.nwk")

#Note that the alpha- and beta-diversity-files needed in Phyloseq.Rmd has been prepared in the step 9.

  11. Figures generated by Phyloseq.Rmd and MicrobiotaProcess_*.R

    The following files can be found under server.

    ./Phyloseq.Rmd (Result Phyloseq.html)
./MicrobiotaProcess_cluster1_Group9-11_vs_cluster2_Group12-14_orig.R
./MicrobiotaProcess_Group1_vs_Group2.R
./MicrobiotaProcess_Group3_vs_Group4.R
./MicrobiotaProcess_PCA_Group1-4.R
./MicrobiotaProcess_PCA_Group9-14.R

  12. Generating relative_abundance_phylum_order_family.xls Convert the Excel file for Phylum, Order, and Family relative abundances for all samples to csv file after correcting the family due to the two redundance species “=SUM(EG10+EG18)” Edit the csv file, merge then to a file.

    ~/Tools/csv2xls-0.4/csv_to_xls.py relative_abundance_phylum.csv relative_abundance_order.csv relative_abundance_family.csv -d$'\t' -o relative_abundance_phylum_order_family.xls;