1, MicrobiotaProcess_Group1_vs_Group5.R
# https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc//MicrobiotaProcess.html
# -----------------------------------
# ---- prepare the R environment ----
#Rscript MicrobiotaProcess.R
#NOTE: exit R script, then login again R-environment; rm -rf Phyloseq*_cache
#mkdir figures
rmarkdown::render('Phyloseq.Rmd',output_file='Phyloseq.html')
# with #alpha = 2.0, running the following script further!
# ("1","2","5","6","7", "15","16","17","18","19","20", "29","30","31","32", "40","41","42","43","44","46")
#div.df2[div.df2 == "Group1"] <- "aged.post"
#div.df2[div.df2 == "Group3"] <- "young.post"
#div.df2[div.df2 == "Group5"] <- "aged.post"
#div.df2[div.df2 == "Group7"] <- "young.post"
# ("8","9","10","12","13","14", "21","22","23","24","25","26","27","28", "33","34","35","36","37","38","39","51", "47","48","49","50","52","53","55")
#div.df2[div.df2 == "Group2"] <- "aged.pre"
#div.df2[div.df2 == "Group4"] <- "young.pre"
#div.df2[div.df2 == "Group6"] <- "aged.pre"
#div.df2[div.df2 == "Group8"] <- "young.pre"
#Group1: f.aged and post
#Group2: f.aged and pre
#Group3: f.young and post
#Group4: f.young and pre
#Group5: m.aged and post
#Group6: m.aged and pre
#Group7: m.young and post
#Group8: m.young and pre
#[,c("1","2","5","6","7", "8","9","10","12","13","14")]
#[,c("15","16","17","18","19","20", "21","22","23","24","25","26","27","28")]
#[,c("29","30","31","32", "33","34","35","36","37","38","39","51")]
#[,c("40","41","42","43","44","46", "47","48","49","50","52","53","55")]
#For the first set:
#a6cee3: This is a light blue color, somewhat pastel and soft.
#b2df8a: A soft, pale green, similar to a light lime.
#fb9a99: A soft pink, slightly peachy or salmon-like.
#cab2d6: A pale purple, reminiscent of lavender or a light mauve.
#For the second set:
#1f78b4: This is a strong, vivid blue, close to cobalt or a medium-dark blue.
#33a02c: A medium forest green, vibrant and leafy.
#e31a1c: A bright red, very vivid, similar to fire engine red.
#6a3d9a: This would be described as a deep purple, akin to a dark lavender or plum.
# -----------------------------
# ---- 3.1. bridges other tools
##https://github.com/YuLab-SMU/MicrobiotaProcess
##https://www.bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc/MicrobiotaProcess.html
##https://chiliubio.github.io/microeco_tutorial/intro.html#framework
##https://yiluheihei.github.io/microbiomeMarker/reference/plot_cladogram.html
#BiocManager::install("MicrobiotaProcess")
#install.packages("microeco")
#install.packages("ggalluvial")
#install.packages("ggh4x")
library(MicrobiotaProcess)
library(microeco)
library(ggalluvial)
library(ggh4x)
library(gghalves)
library(tidyr)
## Convert the phyloseq object to a MicrobiotaProcess object
#mp <- as.MicrobiotaProcess(ps.ng.tax)
#mt <- phyloseq2microeco(ps.ng.tax) #--> ERROR
#abundance_table <- mt$abun_table
#taxonomy_table <- mt$tax_table
#ps.ng.tax_abund <- phyloseq::filter_taxa(ps.ng.tax, function(x) sum(x > total*0.01) > 0, TRUE)
#ps.ng.tax_most = phyloseq::filter_taxa(ps.ng.tax_rel, function(x) mean(x) > 0.001, TRUE)
##OPTION1 (NOT_USED): take all samples, prepare ps.ng.tax_abund --> mpse_abund
##mpse <- ps.ng.tax %>% as.MPSE()
#mpse_abund <- ps.ng.tax_abund %>% as.MPSE()
##OPTION2 (USED!): take partial samples, prepare ps.ng.tax or ps.ng.tax_abund (2 replacements!)--> ps.ng.tax_sel --> mpse_abund
ps.ng.tax_sel <- ps.ng.tax_abund
##otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("1","2","5","6","7", "15","16","17","18","19","20", "29","30","31","32", "40","41","42","43","44","46")]
##NOTE: Only choose Group2, Group4, Group6, Group8
#> ps.ng.tax_sel
#otu_table() OTU Table: [ 37465 taxa and 29 samples ]
#sample_data() Sample Data: [ 29 samples by 10 sample variables ]
#tax_table() Taxonomy Table: [ 37465 taxa by 7 taxonomic ranks ]
#phy_tree() Phylogenetic Tree: [ 37465 tips and 37461 internal nodes ]
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax_abund)[,c("1","2","5","6","7", "29","30","31","32")]
mpse_abund <- ps.ng.tax_sel %>% as.MPSE()
# A MPSE-tibble (MPSE object) abstraction: 2,352 × 20
# NOTE mpse_abund contains 20 variables: OTU, Sample, Abundance, BarcodeSequence, LinkerPrimerSequence, FileInput, Group,
# Sex_age -
# default will display the confidence interval around smooth.
# se=TRUE
# NOTE that two colors #c(“#00A087FF”, “#3C5488FF”) for .group = pre_post_stroke; four colors c(“#1f78b4”, “#33a02c”, “#e31a1c”, “#6a3d9a”) for .group = Group;
p1 <- mpse_abund %>%
mp_plot_rarecurve(
.rare = RareAbundanceRarecurve,
.alpha = Observe,
)
p2 <- mpse_abund %>%
mp_plot_rarecurve(
.rare = RareAbundanceRarecurve,
.alpha = Observe,
.group = Group
) +
scale_color_manual(values=c(“#1f78b4”, “#e31a1c”)) +
scale_fill_manual(values=c(“#1f78b4”, “#e31a1c”), guide=”none”)
# combine the samples belong to the same groups if plot.group=TRUE
p3 <- mpse_abund %>%
mp_plot_rarecurve(
.rare = RareAbundanceRarecurve,
.alpha = “Observe”,
.group = Group,
plot.group = TRUE
) +
scale_color_manual(values=c(“#1f78b4”, “#e31a1c”)) +
scale_fill_manual(values=c(“#1f78b4”, “#e31a1c”),guide=”none”)
png(“rarefaction_of_samples_or_groups.png”, width=1080, height=600)
p1 + p2 + p3
dev.off()
# ——————————————
# 3.3. calculate alpha index and visualization
library(ggplot2)
library(MicrobiotaProcess)
mpse_abund %<>%
mp_cal_alpha(.abundance=RareAbundance)
mpse_abund
#NOTE mpse_abund contains 28 varibles = 22 varibles + Observe
-
# mp_plot_dist provides there methods to visualize the distance between the samples or groups
# when .group is not provided, the dot heatmap plot will be return
p1 <- mpse_abund %>% mp_plot_dist(.distmethod = bray)
png(“distance_between_samples.png”, width= 1000, height=1000)
p1
dev.off()
# when .group is provided, the dot heatmap plot with group information will be return.
p2 <- mpse_abund %>% mp_plot_dist(.distmethod = bray, .group = Group)
# The scale or theme of dot heatmap plot can be adjusted using set_scale_theme function.
p2 %>% set_scale_theme(
x = scale_fill_manual(
values=c(“#1f78b4”, “#e31a1c”), #c(“orange”, “deepskyblue”),
guide = guide_legend(
keywidth = 1,
keyheight = 0.5,
title.theme = element_text(size=8),
label.theme = element_text(size=6)
)
),
aes_var = Group # specific the name of variable
) %>%
set_scale_theme(
x = scale_color_gradient(
guide = guide_legend(keywidth = 0.5, keyheight = 0.5)
),
aes_var = bray
) %>%
set_scale_theme(
x = scale_size_continuous(
range = c(0.1, 3),
guide = guide_legend(keywidth = 0.5, keyheight = 0.5)
),
aes_var = bray
)
png(“distance_between_samples_with_group_info.png”, width= 1000, height=1000)
p2
dev.off()
# when .group is provided and group.test is TRUE, the comparison of different groups will be returned
# Assuming p3 is a ggplot object after mp_plot_dist call
p3 <- mpse_abund %>%
mp_plot_dist(.distmethod = bray, .group = Group, group.test = TRUE, textsize = 6) +
theme(
axis.title.x = element_text(size = 14), # Customize x-axis label face = “bold”
axis.title.y = element_text(size = 14), # Customize y-axis label
axis.text.x = element_text(size = 14), # Customize x-axis ticks
axis.text.y = element_text(size = 14) # Customize y-axis ticks
)
# Save the plot with the new theme settings
png(“Comparison_of_Bray_Distances.png”, width = 1000, height = 1000)
print(p3) # Ensure that p3 is explicitly printed in the device
dev.off()
# Extract Bray-Curtis Distance Values and save them in a Excel-table.
library(dplyr)
library(openxlsx)
# Define the sample numbers vector
sample_numbers <- c("1","2","5","6","7", "29","30","31","32")
# Consolidate the list of tibbles using the actual sample numbers
bray_data <- bind_rows(
lapply(seq_along(mpse_abund$bray), function(i) {
tibble(
Sample1 = sample_numbers[i], # Use actual sample number
Sample2 = mpse_abund$bray[[i]]$braySampley,
BrayDistance = mpse_abund$bray[[i]]$bray
)
}),
.id = "PairID"
)
# Print the data frame to check the output
print(bray_data)
# Write the data frame to an Excel file
write.xlsx(bray_data, file = "Bray_Curtis_Distances.xlsx")
#DELETE the column "PairID" in Excel file
# -----------------------
# 3.5.2 The PCoA analysis
#install.packages("corrr")
library(corrr)
#install.packages("ggside")
library(ggside)
mpse_abund %<>%
mp_cal_pcoa(.abundance=hellinger, distmethod=”bray”)
# The dimensions of ordination analysis will be added the colData slot (default).
mpse_abund
mpse_abund %>% print(width=380, n=2)
#NOTE mpse_abund contains 34 varibles = 31 varibles + `PCo1 (30.16%)`
- , RareAbundanceByGroup
- ]
#> methods(class=class(mpse_abund))
# We also can perform adonis or anosim to check whether it is significant to the dissimilarities of groups.
mpse_abund %<>%
mp_adonis(.abundance=hellinger, .formula=~Group, distmethod=”bray”, permutations=9999, action=”add”)
mpse_abund %>% mp_extract_internal_attr(name=adonis)
#PAUSE
p1 <- mpse_abund %>%
mp_plot_ord(
.ord = pcoa,
.group = Group,
.color = Group,
.size = 2.4,
.alpha = 1,
ellipse = TRUE,
show.legend = FALSE # don’t display the legend of stat_ellipse
) +
scale_fill_manual(
#values = c(“#a6cee3”, “#1f78b4”, “#b2df8a”, “#33a02c”, “#fb9a99”, “#e31a1c”, “#cab2d6”, “#6a3d9a”),
#values = c(“#a6cee3”, “#b2df8a”, “#fb9a99”, “#cab2d6”),
values = c(“#1f78b4”, “#e31a1c”),
guide = guide_legend(keywidth=1.6, keyheight=1.6, label.theme=element_text(size=12))
) +
scale_color_manual(
#values=c(“#a6cee3”, “#1f78b4”, “#b2df8a”, “#33a02c”, “#fb9a99”, “#e31a1c”, “#cab2d6”, “#6a3d9a”),
#values = c(“#a6cee3”, “#b2df8a”, “#fb9a99”, “#cab2d6”),
values = c(“#1f78b4”, “#e31a1c”),
guide = guide_legend(keywidth=1.6, keyheight=1.6, label.theme=element_text(size=12))
)
#scale_fill_manual(values=c(“#FF0000”, “#000000”, “#0000FF”, “#C0C0C0”, “#00FF00”, “#FFFF00”, “#00FFFF”, “#FFA500”)) +
#scale_color_manual(values=c(“#FF0000”, “#000000”, “#0000FF”, “#C0C0C0”, “#00FF00”, “#FFFF00”, “#00FFFF”, “#FFA500”))
#scale_fill_manual(values=c(“#00A087FF”, “#3C5488FF”)) +
#scale_color_manual(values=c(“#00A087FF”, “#3C5488FF”))
#png(“PCoA.png”, width= 1000, height=1000)
#svg(“PCoA.svg”, width= 11, height=10)
#svg(“PCoA_.svg”, width=10, height=10)
#svg(“PCoA.svg”)
pdf(“PCoA.pdf”)
p1
dev.off()
#FF0000: Red
#000000: Black
#0000FF: Blue
#C0C0C0: Silver
#00FF00: Lime (often referred to simply as Green in web colors)
#FFFF00: Yellow
#00FFFF: Aqua (also known as Cyan)
#FFA500: Orange
# The size of point also can be mapped to other variables such as Observe, or Shannon
# Then the alpha diversity and beta diversity will be displayed simultaneously.
p2 <- mpse_abund %>%
mp_plot_ord(
.ord = pcoa,
.group = Group,
.color = Group,
.size = Shannon,
.alpha = Observe,
ellipse = TRUE,
show.legend = FALSE # don’t display the legend of stat_ellipse
) +
scale_fill_manual(
values = c(“#1f78b4”, “#e31a1c”), #only needs four colors.
#values = c(“#FF0000”, “#000000”, “#0000FF”, “#C0C0C0”, “#00FF00”, “#FFFF00”, “#00FFFF”, “#FFA500”),
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
) +
scale_color_manual(
values = c(“#1f78b4”, “#e31a1c”), #only needs four colors.
#values=c(“#FF0000”, “#000000”, “#0000FF”, “#C0C0C0”, “#00FF00”, “#FFFF00”, “#00FFFF”, “#FFA500”),
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
) +
scale_size_continuous(
range=c(0.5, 3),
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
)
pdf(“PCoA2.pdf”)
p2
dev.off()
# Add the sample name as text labels
library(ggrepel)
p2 <- mpse_abund %>%
mp_plot_ord(
.ord = pcoa,
.group = Group,
.color = Group,
.size = Shannon,
.alpha = Observe,
ellipse = TRUE,
show.legend = FALSE # don’t display the legend of stat_ellipse
) +
geom_text_repel(aes(label = ifelse(Sample == “1”, “1”, Sample)), # Prioritize “1”
size = 3,
color = “black”, # Set the label color to black for better visibility
max.overlaps = Inf, # Allow maximum labels
force = 2, # Increase the force to push labels apart
box.padding = 0.5, # Add more padding around the labels
segment.size = 0.2 # Line segment size connecting labels to points
) +
scale_fill_manual(
values = c(“#1f78b4”, “#e31a1c”), # only needs two colors
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
) +
scale_color_manual(
values = c(“#1f78b4”, “#e31a1c”), # only needs two colors
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
) +
scale_size_continuous(
range=c(0.5, 3),
guide = guide_legend(keywidth=0.6, keyheight=0.6, label.theme=element_text(size=8))
)
#pdf(“PCoA2_labeled.pdf”)
png(“PCoA2_labeled.png”, width=800, height=800)
p2
dev.off()
# ——————————————
# 3.5.3 Hierarchical cluster (tree) analysis
#input should contain hellinger!
mpse_abund %<>%
mp_cal_clust(
.abundance = hellinger,
distmethod = “bray”,
hclustmethod = “average”, # (UPGAE)
action = “add” # action is used to control which result will be returned
)
mpse_abund
mpse_abund %>% print(width=380, n=2)
#NOTE mpse_abund contains 34 varibles, no new variable, the column bray has been new calculated!
# if action = ‘add’, the result of hierarchical cluster will be added to the MPSE object
# mp_extract_internal_attr can extract it. It is a treedata object, so it can be visualized
# by ggtree.
sample.clust <- mpse_abund %>% mp_extract_internal_attr(name=’SampleClust’)
#The object contained internal attribute: PCoA ADONIS SampleClust
sample.clust
#–> The associated data tibble abstraction: 27 × 30
library(ggtree)
p <- ggtree(sample.clust) +
geom_tippoint(aes(color=Group)) +
geom_tiplab(as_ylab = TRUE) +
ggplot2::scale_x_continuous(expand=c(0, 0.01))
png("hierarchical_cluster1.png", width= 1000, height=800)
p
dev.off()
#https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc//MicrobiotaProcess.html
# mapping = aes(x = RelRareAbundanceBySample-->Group,
# y = Sample–>Group,
# fill = Phyla
# ),
library(ggtreeExtra)
library(ggplot2)
# Extract relative abundance of phyla
phyla.tb <- mpse_abund %>%
mp_extract_abundance(taxa.class=Phylum, topn=30)
# The abundance of each samples is nested, it can be flatted using the unnest of tidyr.
phyla.tb %<>% tidyr::unnest(cols=RareAbundanceBySample) %>% dplyr::rename(Phyla=”label”)
phyla.tb
phyla.tb %>% print(width=380, n=10)
p1 <- p +
geom_fruit(
data=phyla.tb,
geom=geom_col,
mapping = aes(x = RelRareAbundanceBySample,
y = Sample,
fill = Phyla
),
orientation = "y",
#offset = 0.4,
pwidth = 3,
axis.params = list(axis = "x",
title = "The relative abundance of phyla (%)",
title.size = 4,
text.size = 2,
vjust = 1),
grid.params = list()
)
png("hierarchical_cluster2_Phyla.png", width = 1000, height = 800)
p1
dev.off()
# Extract relative abundance of classes
class.tb <- mpse_abund %>%
mp_extract_abundance(taxa.class = Class, topn = 30)
# Flatten and rename the columns
class.tb %<>% tidyr::unnest(cols = RareAbundanceBySample) %>% dplyr::rename(Class = “label”)
# View the data frame
class.tb
# Create the plot
p1 <- p +
geom_fruit(
data = class.tb,
geom = geom_col,
mapping = aes(x = RelRareAbundanceBySample,
y = Sample,
fill = Class
),
orientation = "y",
pwidth = 3,
axis.params = list(axis = "x",
title = "The relative abundance of classes (%)",
title.size = 4,
text.size = 2,
vjust = 1),
grid.params = list()
)
# Save the plot to a file #ERROR-->NEED to be DEBUGGED!
png(“hierarchical_cluster2_Class.png”, width = 1000, height = 800)
print(p1)
dev.off()
# ———————–
# 3.6 Biomarker discovery
library(ggtree)
library(ggtreeExtra)
library(ggplot2)
library(MicrobiotaProcess)
library(tidytree)
library(ggstar)
library(forcats)
library(writexl)
#—-BUG: why resulting in 26 taxa != 16 in the end —-
mpse_abund %>% print(width=150)
#mpse_abund %<>%
# mp_cal_abundance( # for each samples
# .abundance = RareAbundance
# ) %>%
# mp_cal_abundance( # for each groups
# .abundance=RareAbundance,
# .group=Group
# )
#mpse_abund
mpse_abund %<>%
mp_diff_analysis(
.abundance = RelRareAbundanceBySample,
.group = Group,
cl.min = 4,
first.test.alpha = 0.01, filter.p=”pvalue”
)
# The result is stored to the taxatree or otutree slot, you can use mp_extract_tree to extract the specific slot.
taxa.tree <- mpse_abund %>%
mp_extract_tree(type=”taxatree”)
taxa.tree
## And the result tibble of different analysis can also be extracted with tidytree (>=0.3.5)
#LDAupper, LDAmean, LDAlower,
taxa.tree %>% select(label, nodeClass, Sign_Group, fdr) #%>% dplyr::filter(!is.na(fdr))
taxa.tree %>% print(width=150, n=200)
# — replace the pvalue and fdr with pvalue and p-adjusted from DESeq enrichment results —
#TODO: replace the values of pvalue and fdr in taxa.tree, with the values of pvalue and padj from sigtab, if the the tips in taxa.tree could be found in colnames(sigtab).
#tree_data <- get.data(taxa.tree)
#as.treedata(taxa.tree)
#d <- tibble(label = paste0('t', 1:4), trait = rnorm(4))
tree_data <- as_tibble(taxa.tree)
#full_join(x, d, by = 'label') %>% as.treedata
# — NOTE that sigtab generated by Phyloseq.Rmd should take ‘alpha = 2.0’ —
# Modify tree_data by joining with sigtab and updating Sign_Group
sigtab$label <- rownames(sigtab)
write.xlsx(sigtab, file = "sigtab.xlsx")
sum(sigtab$padj<0.05)
#taxa.tree <- left_join(tree_data, sigtab[, c("label", "log2FoldChange", "pvalue", "padj")], by = 'label') %>% as.treedata
taxa.tree2 <- tree_data %>%
left_join(sigtab[, c(“label”, “baseMean”, “log2FoldChange”, “lfcSE”, “stat”, “pvalue”, “padj”)], by = “label”) %>%
mutate(Sign_Group = case_when(
log2FoldChange > 0 & padj <= 0.05 ~ "Group1",
log2FoldChange < 0 & padj <= 0.05 ~ "Group5",
TRUE ~ NA_character_ # Sets Sign_Group to NA otherwise
)) %>%
as.treedata() # Convert the dataframe to a treedata object
taxa.tree2 %>% print(width=380, n=20)
# —- print taxa_data2 to Excel, why resulting in 26 records? —-
taxa_data2 <- as_tibble(taxa.tree2)
sum(!is.na(taxa_data2$Sign_Group))
sapply(taxa_data2, class)
# Remove or transform list columns if not needed
taxa_data2_simplified <- taxa_data2 %>%
select(-RareAbundanceBySample, -RareAbundanceByGroup) %>%
mutate(across(where(is.list), ~toString(.))) # Convert lists to character strings if needed
# Replace NA with a placeholder, such as “NA” or another suitable representation
taxa_data2_simplified <- taxa_data2_simplified %>%
mutate(across(everything(), ~ifelse(is.na(.), “NA”, .)))
taxonomy_data <- as.data.frame(mp_extract_taxonomy(mpse_abund))
colnames(taxa_data2_simplified)[colnames(taxa_data2_simplified) == "label"] <- "OTU"
combined_data <- left_join(taxa_data2_simplified, taxonomy_data, by = "OTU")
write_xlsx(combined_data, "taxa_data2.xlsx")
#(UNDER HOST-ENV) cp sigtab.xlsx diff_analysis_Group1_vs_Group5.xlsx and then switch label as the 1st column and sort the columns by padj.
# -- NOTE that sometimes the record in DESeq2 not occurs in the final list, since the statistics calculation of MicrobiotaProcess results in NA, e.g. the record FJ879443.1.1488, we can simply delete the record from diff_analysis_Group1_vs_Group5.xlsx --
# Since taxa.tree is treedata object, it can be visualized by ggtree and ggtreeExtra
p1 <- ggtree(
taxa.tree2,
layout="radial",
size = 0.3
) +
geom_point(
data = td_filter(!isTip),
fill="white",
size=1,
shape=21
)
# display the high light of phylum clade.
p2 <- p1 +
geom_hilight(
data = td_filter(nodeClass == "Phylum"),
mapping = aes(node = node, fill = label)
)
# display the relative abundance of features(OTU)
p3 <- p2 +
ggnewscale::new_scale("fill") +
geom_fruit(
data = td_unnest(RareAbundanceBySample),
geom = geom_star,
mapping = aes(
x = fct_reorder(Sample, Group, .fun=min),
size = RelRareAbundanceBySample,
fill = Group,
subset = RelRareAbundanceBySample > 0
),
starshape = 13,
starstroke = 0.25,
offset = 0.03,
pwidth = 0.4,
grid.params = list(linetype=2)
) +
scale_size_continuous(
name=”Relative Abundance (%)”,
range = c(.5, 3)
) +
scale_fill_manual(values=c(“#1B9E77”, “#D95F02”))
# display the tip labels of taxa tree
p4 <- p3 + geom_tiplab(size=6, offset=4.0)
# display the LDA of significant OTU.
#p5 <- p4 +
# ggnewscale::new_scale("fill") +
# geom_fruit(
# geom = geom_col,
# mapping = aes(
# x = LDAmean,
# fill = Sign_Group,
# subset = !is.na(LDAmean)
# ),
# orientation = "y",
# offset = 0.3,
# pwidth = 0.5,
# axis.params = list(axis = "x",
# title = "Log10(LDA)",
# title.height = 0.01,
# title.size = 2,
# text.size = 1.8,
# vjust = 1),
# grid.params = list(linetype = 2)
# )
# display the significant (FDR-->pvalue–>padj) taxonomy after kruskal.test (default)
#shape = 21,
#scale_size_continuous(range=c(1, 3)) +
p6 <- p4 +
ggnewscale::new_scale("size") +
geom_point(
data=td_filter(!is.na(Sign_Group)),
mapping = aes(size = -log10(padj),
fill = Sign_Group,
),
shape = 21,
) +
scale_size_continuous(range=c(1, 4)) +
scale_fill_manual(values=c("#1B9E77", "#D95F02"))
svg("diff_analysis.svg",width=22, height=22)
#png("differently_expressed_otu.png", width=2000, height=2000)
p6 + theme(
legend.key.height = unit(1.0, "cm"),
legend.key.width = unit(1.0, "cm"),
legend.spacing.y = unit(0.01, "cm"),
legend.text = element_text(size = 20),
legend.title = element_text(size = 20)
#legend.position = c(0.99, 0.01)
)
dev.off()
2, Phyloseq.Rmd
---
title: "Phyloseq microbiome"
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, echo=FALSE, warning=FALSE}
## Global options
# TODO: reproduce the html with the additional figure/SVN-files for editing.
# IMPORTANT NOTE: needs before "mkdir figures"
#rmarkdown::render('Phyloseq.Rmd',output_file='Phyloseq.html')
```
```{r load-packages, include=FALSE}
library(knitr)
library(rmdformats)
library(readxl)
library(dplyr)
library(kableExtra)
options(max.print="75")
knitr::opts_chunk$set(fig.width=8,
fig.height=6,
eval=TRUE,
cache=TRUE,
echo=TRUE,
prompt=FALSE,
tidy=TRUE,
comment=NA,
message=FALSE,
warning=FALSE)
opts_knit$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
```
# Data
Import raw data and assign sample key:
```{r, echo=TRUE, warning=FALSE}
#extend map_corrected.txt with Diet and Flora
#setwd("~/DATA/Data_Laura_16S_2/core_diversity_e4753")
map_corrected <- read.csv("../map_corrected.txt", 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}
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)
“`
# Read the data and create phyloseq objects
Three tables are needed
* OTU
* Taxonomy
* Samples
“`{r, echo=TRUE, warning=FALSE}
#Change your working directory to where the files are located
ps.ng.tax <- import_biom("./table_even42369.biom", "../clustering/rep_set.tre")
sample <- read.csv("../map_corrected.txt", sep="\t", row.names=1)
SAM = sample_data(sample, errorIfNULL = T)
rownames(SAM) <-
c("1","2","3","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","40","41","42","43","44","46","47","48","49","50","51","52","53","55")
ps.ng.tax <- merge_phyloseq(ps.ng.tax, SAM)
print(ps.ng.tax)
colnames(tax_table(ps.ng.tax)) <- c("Domain","Phylum","Class","Order","Family","Genus","Species")
saveRDS(ps.ng.tax, "./ps.ng.tax.rds")
```
Visualize data
```{r, echo=TRUE, warning=FALSE}
sample_names(ps.ng.tax)
rank_names(ps.ng.tax)
sample_variables(ps.ng.tax)
```
Normalize number of reads in each sample using median sequencing depth.
```{r, echo=TRUE, warning=FALSE}
# RAREFACTION
#set.seed(9242) # This will help in reproducing the filtering and nomalisation.
#ps.ng.tax <- rarefy_even_depth(ps.ng.tax, sample.size = 42369)
#total <- 42369
# 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.ng.tax_rel <- microbiome::transform(ps.ng.tax, "compositional")
saveRDS(ps.ng.tax, "./ps.ng.tax.rds")
hmp.meta <- meta(ps.ng.tax)
hmp.meta$sam_name <- rownames(hmp.meta)
```
# Heatmaps
```{r, echo=TRUE, warning=FALSE}
#MOVE_FROM_ABOVE: The number of reads used for normalization is **`r sprintf("%.0f", total)`**.
#A basic heatmap using the default parameters.
# plot_heatmap(ps.ng.tax, method = "NMDS", distance = "bray")
#NOTE that giving the correct OTU numbers in the text (1%, 0.5%, ...)!!!
```
We consider the most abundant OTUs for heatmaps. For example one can only take OTUs that represent at least 1% of reads in at least one sample. Remember we normalized all the sampples to median number of reads (total). We are left with only 168 OTUS which makes the reading much more easy.
```{r, echo=TRUE, warning=FALSE}
# Custom function to plot a heatmap with the specified sample order
#plot_heatmap_custom <- function(ps, sample_order, method = "NMDS", distance = "bray") {
ps.ng.tax_abund <- phyloseq::filter_taxa(ps.ng.tax, function(x) sum(x > total*0.01) > 0, TRUE)
kable(otu_table(ps.ng.tax_abund)) %>%
kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
# Calculate the relative abundance for each sample
ps.ng.tax_abund_rel <- transform_sample_counts(ps.ng.tax_abund, function(x) x / sum(x))
datamat_ = as.data.frame(otu_table(ps.ng.tax_abund))
#datamat <- datamat_[c("1","2","5","6","7", "8","9","10","12","13","14", "15","16","17","18","19","20", "21","22","23","24","25","26","27","28", "29","30","31","32", "33","34","35","36","37","38","39","51", "40","41","42","43","44","46", "47","48","49","50","52","53","55")]
datamat <- datamat_[c("8","9","10","12","13","14", "21","22","23","24","25","26","27","28", "33","34","35","36","37","38","39","51", "47","48","49","50","52","53","55")]
hr <- hclust(as.dist(1-cor(t(datamat), method="pearson")), method="complete")
hc <- hclust(as.dist(1-cor(datamat, method="spearman")), method="complete")
mycl = cutree(hr, h=max(hr$height)/1.08)
mycol = c("YELLOW", "DARKBLUE", "DARKORANGE", "DARKMAGENTA", "DARKCYAN", "DARKRED", "MAROON", "DARKGREEN", "LIGHTBLUE", "PINK", "MAGENTA", "LIGHTCYAN","LIGHTGREEN", "BLUE", "ORANGE", "CYAN", "RED", "GREEN");
mycol = mycol[as.vector(mycl)]
sampleCols <- rep('GREY',ncol(datamat))
#names(sampleCols) <- c("Group1", "Group1", "Group1", "Group1", "Group1", "Group2", "Group2", "Group2", "Group2", "Group2","Group2", "Group3", "Group3", "Group3", "Group3", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1", "Group1")
#sampleCols[colnames(datamat)=='1'] <- '#a6cee3'
#sampleCols[colnames(datamat)=='2'] <- '#a6cee3'
#sampleCols[colnames(datamat)=='5'] <- '#a6cee3'
#sampleCols[colnames(datamat)=='6'] <- '#a6cee3'
#sampleCols[colnames(datamat)=='7'] <- '#a6cee3'
sampleCols[colnames(datamat)=='8'] <- '#1f78b4'
sampleCols[colnames(datamat)=='9'] <- '#1f78b4'
sampleCols[colnames(datamat)=='10'] <- '#1f78b4'
sampleCols[colnames(datamat)=='12'] <- '#1f78b4'
sampleCols[colnames(datamat)=='13'] <- '#1f78b4'
sampleCols[colnames(datamat)=='14'] <- '#1f78b4'
#sampleCols[colnames(datamat)=='15'] <- '#b2df8a'
#sampleCols[colnames(datamat)=='16'] <- '#b2df8a'
#sampleCols[colnames(datamat)=='17'] <- '#b2df8a'
#sampleCols[colnames(datamat)=='18'] <- '#b2df8a'
#sampleCols[colnames(datamat)=='19'] <- '#b2df8a'
#sampleCols[colnames(datamat)=='20'] <- '#b2df8a'
sampleCols[colnames(datamat)=='21'] <- '#33a02c'
sampleCols[colnames(datamat)=='22'] <- '#33a02c'
sampleCols[colnames(datamat)=='23'] <- '#33a02c'
sampleCols[colnames(datamat)=='24'] <- '#33a02c'
sampleCols[colnames(datamat)=='25'] <- '#33a02c'
sampleCols[colnames(datamat)=='26'] <- '#33a02c'
sampleCols[colnames(datamat)=='27'] <- '#33a02c'
sampleCols[colnames(datamat)=='28'] <- '#33a02c'
#sampleCols[colnames(datamat)=='29'] <- '#fb9a99'
#sampleCols[colnames(datamat)=='30'] <- '#fb9a99'
#sampleCols[colnames(datamat)=='31'] <- '#fb9a99'
#sampleCols[colnames(datamat)=='32'] <- '#fb9a99'
sampleCols[colnames(datamat)=='33'] <- '#e31a1c'
sampleCols[colnames(datamat)=='34'] <- '#e31a1c'
sampleCols[colnames(datamat)=='35'] <- '#e31a1c'
sampleCols[colnames(datamat)=='36'] <- '#e31a1c'
sampleCols[colnames(datamat)=='37'] <- '#e31a1c'
sampleCols[colnames(datamat)=='38'] <- '#e31a1c'
sampleCols[colnames(datamat)=='39'] <- '#e31a1c'
sampleCols[colnames(datamat)=='51'] <- '#e31a1c'
#sampleCols[colnames(datamat)=='40'] <- '#cab2d6'
#sampleCols[colnames(datamat)=='41'] <- '#cab2d6'
#sampleCols[colnames(datamat)=='42'] <- '#cab2d6'
#sampleCols[colnames(datamat)=='43'] <- '#cab2d6'
#sampleCols[colnames(datamat)=='44'] <- '#cab2d6'
#sampleCols[colnames(datamat)=='46'] <- '#cab2d6'
sampleCols[colnames(datamat)=='47'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='48'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='49'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='50'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='52'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='53'] <- '#6a3d9a'
sampleCols[colnames(datamat)=='55'] <- '#6a3d9a'
#bluered(75)
#color_pattern <- colorRampPalette(c("blue", "white", "red"))(100)
library(RColorBrewer)
custom_palette <- colorRampPalette(brewer.pal(9, "Blues"))
heatmap_colors <- custom_palette(100)
#colors <- heatmap_color_default(100)
png("figures/heatmap.png", width=1200, height=2400)
#par(mar=c(2, 2, 2, 2)) , lwid=1 lhei=c(0.7, 10)) # Adjust height of color keys keysize=0.3,
heatmap.2(as.matrix(datamat),Rowv=as.dendrogram(hr),Colv = NA, dendrogram = 'row',
scale='row',trace='none',col=heatmap_colors, cexRow=1.2, cexCol=1.5,
RowSideColors = mycol, ColSideColors = sampleCols, srtCol=15, labRow=row.names(datamat), key=TRUE, margins=c(10, 15), lhei=c(0.7, 15), lwid=c(1,8))
dev.off()
```
```{r, echo=TRUE, warning=FALSE, fig.cap="Heatmap", out.width = '100%', fig.align= "center"}
knitr::include_graphics("./figures/heatmap.png")
```
```{r, echo=FALSE, warning=FALSE}
#It is possible to use different distances and different multivaraite methods. Many different built-in distances can be used.
#dist_methods <- unlist(distanceMethodList)
#print(dist_methods)
```
\pagebreak
# Taxonomic summary
## Bar plots in phylum level
```{r, echo=FALSE, warning=FALSE}
#Make the bargraph nicer by removing OTUs boundaries. This is done by adding ggplot2 modifier.
# 1: uniform color. Color is for the border, fill is for the inside
#ggplot(mtcars, aes(x=as.factor(cyl) )) +
# geom_bar(color="blue", fill=rgb(0.1,0.4,0.5,0.7) )
# 2: Using Hue
#ggplot(mtcars, aes(x=as.factor(cyl), fill=as.factor(cyl) )) +
# geom_bar( ) +
# scale_fill_hue(c = 40) +
# theme(legend.position="none")
# 3: Using RColorBrewer
#ggplot(mtcars, aes(x=as.factor(cyl), fill=as.factor(cyl) )) +
# geom_bar( ) +
# scale_fill_brewer(palette = "Set1") +
# theme(legend.position="none")
# 4: Using greyscale:
#ggplot(mtcars, aes(x=as.factor(cyl), fill=as.factor(cyl) )) +
# geom_bar( ) +
# scale_fill_grey(start = 0.25, end = 0.75) +
# theme(legend.position="none")
# 5: Set manualy
#ggplot(mtcars, aes(x=as.factor(cyl), fill=as.factor(cyl) )) +
# geom_bar( ) +
# scale_fill_manual(values = c("red", "green", "blue") ) +
# theme(legend.position="none")
#NOT SUCCESSFUL!
#allGroupsColors<- c(
# "grey0", "grey50", "dodgerblu", "deepskyblue",
# "red", "darkred", "green", "green4")
# plot_bar(ps.ng.tax_rel, fill="Phylum") +
# geom_bar(stat="identity", position="stack") + scale_color_manual(values = allGroupsColors) #, fill=Phylum + scale_fill_brewer(palette = "Set1")
# ##### Keep only the most abundant phyla and
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Actinobacteria")) #1.57
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Bacteroidetes")) #27.27436
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Cyanobacteria")) #0.02244249
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Epsilonbacteraeota")) #0.01309145
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Euryarchaeota")) #0.1210024
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Firmicutes")) #32.50589
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Lentisphaerae")) #0.0001870208
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Patescibacteria")) #0.008789976
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Planctomycetes")) #0.01365252
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Proteobacteria")) #6.769216
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Synergistetes")) #0.005049561
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Tenericutes")) #0.0005610623
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Verrucomicrobia")) #2.076304
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c(NA)) #sum(otu_table(ps.ng.tax_most)) = 2.619413
```
```{r, echo=TRUE, warning=FALSE}
library(ggplot2)
geom.text.size = 6
theme.size = 8 #(14/5) * geom.text.size
#ps.ng.tax_most <- subset_taxa(ps.ng.tax_rel, Phylum %in% c("D_1__Actinobacteria", "D_1__Bacteroidetes", "D_1__Firmicutes", "D_1__Proteobacteria", "D_1__Verrucomicrobia", NA))
ps.ng.tax_most = phyloseq::filter_taxa(ps.ng.tax_rel, function(x) mean(x) > 0.001, TRUE)
#CONSOLE(OPTIONAL): for sampleid 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; do
#echo “otu_table(ps.ng.tax_most)[,${sampleid}]=otu_table(ps.ng.tax_most)[,${sampleid}]/sum(otu_table(ps.ng.tax_most)[,${sampleid}])” done
#OR
ps.ng.tax_most_ = transform_sample_counts(ps.ng.tax_most, function(x) x / sum(x))
“`
“`{r, echo=FALSE, warning=FALSE}
##–Creating 100% stacked bar plots with less abundant taxa in a sub-category #901–
##https://github.com/joey711/phyloseq/issues/901
##ps.ng.tax_most_df <- psmelt(ps.ng.tax_most_) #5986x19
#glom <- tax_glom(ps.ng.tax_most_, taxrank = 'Phylum')
#tax_table(glom) # should list # taxa as # phyla
#data <- psmelt(glom) # create dataframe from phyloseq object
#data$Phylum <- as.character(data$Phylum) #convert to character
##simple way to rename phyla with < 1% abundance
#data$Phylum[data$Abundance < 0.001] <- "< 0.1% abund."
#
#library(plyr)
#medians <- ddply(data, ~Phylum, function(x) c(median=median(x$Abundance)))
#remainder <- medians[medians$median <= 0.001,]$Phylum
#data[data$Phylum %in% remainder,]$Phylum <- "Phyla < 0.1% abund."
#data$Phylum[data$Abundance < 0.001] <- "Phyla < 0.1% abund."
##--> data are not used!
#
##in class level
#glom <- tax_glom(ps.ng.tax_most_, taxrank = 'Class')
#tax_table(glom) # should list # taxa as # phyla
#data <- psmelt(glom) # create dataframe from phyloseq object
#data$Class <- as.character(data$Class) #convert to character
#
##simple way to rename phyla with < 1% abundance
#data$Class[data$Abundance < 0.001] <- "< 0.1% abund."
#Count = length(unique(data$Class))
#
##unique(data$Class)
##data$Class <- factor(data$Class, levels = c("Bacilli", "Bacteroidia", "Verrucomicrobiae", "Clostridia", "Gammaproteobacteria", "Alphaproteobacteria", "Actinobacteria", "Negativicutes", "Erysipelotrichia", "Methanobacteria", "< 0.1% abund."))
##------- Creating 100% stacked bar plots END --------
library(stringr)
#FITTING1:
# tax_table(ps.ng.tax_most_)[1,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Domain"], "__")[[1]][2]
# ... ...
# tax_table(ps.ng.tax_most_)[167,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Species"], "__")[[1]][2]
#ps.ng.tax_most_
#in total [ 89 taxa and 55 samples ]
#otu_table() OTU Table: [ 166 taxa and 54 samples ]
#otu_table() OTU Table: [ 168 taxa and 50 samples ]
#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; do
#echo "tax_table(ps.ng.tax_most_)[${id},\"Domain\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Domain\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Phylum\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Phylum\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Class\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Class\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Order\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Order\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Family\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Family\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Genus\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Genus\"], \"__\")[[1]][2]"
#echo "tax_table(ps.ng.tax_most_)[${id},\"Species\"] <- str_split(tax_table(ps.ng.tax_most_)[${id},\"Species\"], \"__\")[[1]][2]"
#done
tax_table(ps.ng.tax_most_)[1,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[1,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[1,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[2,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[2,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[3,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[3,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[4,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[4,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[5,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[5,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[6,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[6,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[7,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[7,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[8,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[8,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[9,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[9,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[10,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[10,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[11,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[11,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[12,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[12,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[13,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[13,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[14,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[14,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[15,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[15,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[16,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[16,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[17,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[17,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[18,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[18,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[19,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[19,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[20,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[20,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[21,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[21,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[22,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[22,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[23,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[23,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[24,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[24,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[25,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[25,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[26,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[26,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[27,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[27,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[28,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[28,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[29,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[29,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[30,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[30,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[31,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[31,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[32,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[32,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[33,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[33,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[34,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[34,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[35,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[35,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[36,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[36,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[37,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[37,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[38,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[38,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[39,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[39,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[40,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[40,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[41,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[41,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[42,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[42,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[43,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[43,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[44,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[44,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[45,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[45,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[46,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[46,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[47,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[47,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[48,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[48,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[49,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[49,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[50,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[50,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[51,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[51,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[52,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[52,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[53,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[53,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[54,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[54,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[55,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[55,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[56,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[56,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[57,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[57,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[58,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[58,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[59,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[59,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[60,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[60,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[61,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[61,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[62,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[62,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[63,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[63,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[64,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[64,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[65,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[65,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[66,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[66,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[67,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[67,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[68,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[68,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[69,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[69,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[70,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[70,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[71,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[71,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[72,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[72,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[73,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[73,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[74,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[74,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[75,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[75,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[76,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[76,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[77,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[77,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[78,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[78,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[79,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[79,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[80,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[80,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[81,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[81,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[82,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[82,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[83,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[83,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[84,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[84,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[85,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[85,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[86,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[86,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[87,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[87,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[88,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[88,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[89,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[89,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[90,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[90,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[91,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[91,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[92,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[92,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[93,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[93,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[94,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[94,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[95,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[95,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[96,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[96,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[97,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[97,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[98,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[98,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[99,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[99,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[100,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[100,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[101,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[101,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[102,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[102,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[103,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[103,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[104,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[104,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[105,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[105,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[106,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[106,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[107,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[107,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[108,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[108,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[109,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[109,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[110,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[110,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[111,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[111,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[112,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[112,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[113,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[113,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[114,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[114,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[115,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[115,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[116,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[116,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[117,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[117,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[118,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[118,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[119,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[119,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[120,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[120,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[121,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[121,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[122,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[122,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[123,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[123,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[124,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[124,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[125,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[125,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[126,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[126,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[127,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[127,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[128,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[128,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[129,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[129,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[130,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[130,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[131,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[131,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[132,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[132,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[133,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[133,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[134,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[134,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[135,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[135,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[136,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[136,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[137,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[137,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[138,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[138,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[139,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[139,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[140,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[140,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[141,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[141,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[142,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[142,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[143,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[143,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[144,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[144,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[145,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[145,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[146,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[146,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[147,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[147,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[148,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[148,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[149,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[149,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[150,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[150,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[151,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[151,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[152,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[152,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[153,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[153,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[154,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[154,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[155,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[155,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[156,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[156,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[157,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[157,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[158,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[158,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[159,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[159,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[160,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[160,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[161,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[161,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[162,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[162,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[163,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[163,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[164,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[164,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[165,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[165,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[166,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[166,"Species"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Domain"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Domain"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Phylum"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Phylum"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Class"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Class"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Order"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Order"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Family"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Family"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Genus"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Genus"], "__")[[1]][2]
tax_table(ps.ng.tax_most_)[167,"Species"] <- str_split(tax_table(ps.ng.tax_most_)[167,"Species"], "__")[[1]][2]
```
```{r, echo=TRUE, warning=FALSE}
#aes(color="Phylum", fill="Phylum") --> aes()
#ggplot(data=data, aes(x=Sample, y=Abundance, fill=Phylum))
plot_bar(ps.ng.tax_most_, fill=”Phylum”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = 5, colour=”black”)) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=2)) #6 instead of theme.size
“`
“`{r, echo=FALSE, warning=FALSE}
#png(“abc.png”)
#knitr::include_graphics(“./Phyloseq_files/figure-html/unnamed-chunk-7-1.png”)
#dev.off()
“`
\pagebreak
Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.
“`{r, echo=TRUE, warning=FALSE}
ps.ng.tax_most_pre_post_stroke <- merge_samples(ps.ng.tax_most_, "pre_post_stroke")
ps.ng.tax_most_pre_post_stroke_ = transform_sample_counts(ps.ng.tax_most_pre_post_stroke, function(x) x / sum(x))
#plot_bar(ps.ng.tax_most_SampleType_, fill = "Phylum") + geom_bar(aes(color=Phylum, fill=Phylum), stat="identity", position="stack")
plot_bar(ps.ng.tax_most_pre_post_stroke_, fill="Phylum") + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = 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")) + theme(axis.text = element_text(size = theme.size, colour="black"))
```
\pagebreak
Use color according to phylum. Do separate panels Stroke and Sex_age.
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_most_copied <- data.table::copy(ps.ng.tax_most_)
#FITTING6: regulate the bar height if it has replicates: 5+6+6+8+4+8+6+7=25+25=50
otu_table(ps.ng.tax_most_)[,c("1")] <- otu_table(ps.ng.tax_most_)[,c("1")]/5
otu_table(ps.ng.tax_most_)[,c("2")] <- otu_table(ps.ng.tax_most_)[,c("2")]/5
otu_table(ps.ng.tax_most_)[,c("5")] <- otu_table(ps.ng.tax_most_)[,c("5")]/5
otu_table(ps.ng.tax_most_)[,c("6")] <- otu_table(ps.ng.tax_most_)[,c("6")]/5
otu_table(ps.ng.tax_most_)[,c("7")] <- otu_table(ps.ng.tax_most_)[,c("7")]/5
otu_table(ps.ng.tax_most_)[,c("8")] <- otu_table(ps.ng.tax_most_)[,c("8")]/6
otu_table(ps.ng.tax_most_)[,c("9")] <- otu_table(ps.ng.tax_most_)[,c("9")]/6
otu_table(ps.ng.tax_most_)[,c("10")] <- otu_table(ps.ng.tax_most_)[,c("10")]/6
otu_table(ps.ng.tax_most_)[,c("12")] <- otu_table(ps.ng.tax_most_)[,c("12")]/6
otu_table(ps.ng.tax_most_)[,c("13")] <- otu_table(ps.ng.tax_most_)[,c("13")]/6
otu_table(ps.ng.tax_most_)[,c("14")] <- otu_table(ps.ng.tax_most_)[,c("14")]/6
otu_table(ps.ng.tax_most_)[,c("15")] <- otu_table(ps.ng.tax_most_)[,c("15")]/6
otu_table(ps.ng.tax_most_)[,c("16")] <- otu_table(ps.ng.tax_most_)[,c("16")]/6
otu_table(ps.ng.tax_most_)[,c("17")] <- otu_table(ps.ng.tax_most_)[,c("17")]/6
otu_table(ps.ng.tax_most_)[,c("18")] <- otu_table(ps.ng.tax_most_)[,c("18")]/6
otu_table(ps.ng.tax_most_)[,c("19")] <- otu_table(ps.ng.tax_most_)[,c("19")]/6
otu_table(ps.ng.tax_most_)[,c("20")] <- otu_table(ps.ng.tax_most_)[,c("20")]/6
otu_table(ps.ng.tax_most_)[,c("21")] <- otu_table(ps.ng.tax_most_)[,c("21")]/8
otu_table(ps.ng.tax_most_)[,c("22")] <- otu_table(ps.ng.tax_most_)[,c("22")]/8
otu_table(ps.ng.tax_most_)[,c("23")] <- otu_table(ps.ng.tax_most_)[,c("23")]/8
otu_table(ps.ng.tax_most_)[,c("24")] <- otu_table(ps.ng.tax_most_)[,c("24")]/8
otu_table(ps.ng.tax_most_)[,c("25")] <- otu_table(ps.ng.tax_most_)[,c("25")]/8
otu_table(ps.ng.tax_most_)[,c("26")] <- otu_table(ps.ng.tax_most_)[,c("26")]/8
otu_table(ps.ng.tax_most_)[,c("27")] <- otu_table(ps.ng.tax_most_)[,c("27")]/8
otu_table(ps.ng.tax_most_)[,c("28")] <- otu_table(ps.ng.tax_most_)[,c("28")]/8
otu_table(ps.ng.tax_most_)[,c("29")] <- otu_table(ps.ng.tax_most_)[,c("29")]/4
otu_table(ps.ng.tax_most_)[,c("30")] <- otu_table(ps.ng.tax_most_)[,c("30")]/4
otu_table(ps.ng.tax_most_)[,c("31")] <- otu_table(ps.ng.tax_most_)[,c("31")]/4
otu_table(ps.ng.tax_most_)[,c("32")] <- otu_table(ps.ng.tax_most_)[,c("32")]/4
otu_table(ps.ng.tax_most_)[,c("33")] <- otu_table(ps.ng.tax_most_)[,c("33")]/8
otu_table(ps.ng.tax_most_)[,c("34")] <- otu_table(ps.ng.tax_most_)[,c("34")]/8
otu_table(ps.ng.tax_most_)[,c("35")] <- otu_table(ps.ng.tax_most_)[,c("35")]/8
otu_table(ps.ng.tax_most_)[,c("36")] <- otu_table(ps.ng.tax_most_)[,c("36")]/8
otu_table(ps.ng.tax_most_)[,c("37")] <- otu_table(ps.ng.tax_most_)[,c("37")]/8
otu_table(ps.ng.tax_most_)[,c("38")] <- otu_table(ps.ng.tax_most_)[,c("38")]/8
otu_table(ps.ng.tax_most_)[,c("39")] <- otu_table(ps.ng.tax_most_)[,c("39")]/8
otu_table(ps.ng.tax_most_)[,c("51")] <- otu_table(ps.ng.tax_most_)[,c("51")]/8
otu_table(ps.ng.tax_most_)[,c("40")] <- otu_table(ps.ng.tax_most_)[,c("40")]/6
otu_table(ps.ng.tax_most_)[,c("41")] <- otu_table(ps.ng.tax_most_)[,c("41")]/6
otu_table(ps.ng.tax_most_)[,c("42")] <- otu_table(ps.ng.tax_most_)[,c("42")]/6
otu_table(ps.ng.tax_most_)[,c("43")] <- otu_table(ps.ng.tax_most_)[,c("43")]/6
otu_table(ps.ng.tax_most_)[,c("44")] <- otu_table(ps.ng.tax_most_)[,c("44")]/6
otu_table(ps.ng.tax_most_)[,c("46")] <- otu_table(ps.ng.tax_most_)[,c("46")]/6
otu_table(ps.ng.tax_most_)[,c("47")] <- otu_table(ps.ng.tax_most_)[,c("47")]/7
otu_table(ps.ng.tax_most_)[,c("48")] <- otu_table(ps.ng.tax_most_)[,c("48")]/7
otu_table(ps.ng.tax_most_)[,c("49")] <- otu_table(ps.ng.tax_most_)[,c("49")]/7
otu_table(ps.ng.tax_most_)[,c("50")] <- otu_table(ps.ng.tax_most_)[,c("50")]/7
otu_table(ps.ng.tax_most_)[,c("52")] <- otu_table(ps.ng.tax_most_)[,c("52")]/7
otu_table(ps.ng.tax_most_)[,c("53")] <- otu_table(ps.ng.tax_most_)[,c("53")]/7
otu_table(ps.ng.tax_most_)[,c("55")] <- otu_table(ps.ng.tax_most_)[,c("55")]/7
#plot_bar(ps.ng.tax_most_swab_, x="Phylum", fill = "Phylum", facet_grid = Patient~RoundDay) + geom_bar(aes(color=Phylum, fill=Phylum), stat="identity", position="stack") + theme(axis.text = element_text(size = theme.size, colour="black"))
plot_bar(ps.ng.tax_most_, x="Phylum", fill="Phylum", facet_grid = pre_post_stroke~Sex_age) + geom_bar(aes(), stat="identity", position="stack") +
scale_fill_manual(values = 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")) + theme(axis.text = element_text(size = 5, colour="black"), axis.text.x=element_blank(), axis.ticks=element_blank()) + theme(legend.position="bottom") + guides(fill=guide_legend(nrow=2))
```
```{r, echo=FALSE, warning=FALSE}
#knitr::include_graphics("./Phyloseq_files/figure-html/unnamed-chunk-10-1.png")
#> tax_table(carbom)
#Taxonomy Table: [205 taxa by 7 taxonomic ranks]:
# Domain Supergroup Division Class
#Otu001 “Eukaryota” “Archaeplastida” “Chlorophyta” “Mamiellophyceae”
# Order Family Genus
#Otu001 “Mamiellales” “Bathycoccaceae” “Ostreococcus”
#sample_data(ps.ng.tax)
“`
## Bar plots in class level
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_copied, fill=”Class”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = 5, 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.
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_pre_post_stroke_, fill=”Class”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = theme.size, colour=”black”))
“`
\pagebreak
Use color according to class. Do separate panels Stroke and Sex_age.
“`{r, echo=TRUE, warning=FALSE}
#– If existing replicates, to be processed as follows —
plot_bar(ps.ng.tax_most_, x=”Class”, fill=”Class”, facet_grid = pre_post_stroke~Sex_age) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = 5, colour=”black”), axis.text.x=element_blank(), axis.ticks=element_blank()) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=3))
“`
## Bar plots in order level
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_copied, fill=”Order”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = 5, 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.
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_pre_post_stroke_, fill=”Order”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = theme.size, colour=”black”)) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=4))
“`
\pagebreak
Use color according to order. Do separate panels Stroke and Sex_age.
“`{r, echo=TRUE, warning=FALSE}
#FITTING7: regulate the bar height if it has replicates
plot_bar(ps.ng.tax_most_, x=”Order”, fill=”Order”, facet_grid = pre_post_stroke~Sex_age) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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”)) + theme(axis.text = element_text(size = 5, colour=”black”), axis.text.x=element_blank(), axis.ticks=element_blank()) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=4))
“`
## Bar plots in family level
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_copied, fill=”Family”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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″)) + theme(axis.text = element_text(size = 5, 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.
“`{r, echo=TRUE, warning=FALSE}
plot_bar(ps.ng.tax_most_pre_post_stroke_, fill=”Family”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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″)) + theme(axis.text = element_text(size = theme.size, colour=”black”)) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=8))
“`
\pagebreak
Use color according to family. Do separate panels Stroke and Sex_age.
“`{r, echo=TRUE, warning=FALSE}
#– If existing replicates, to be processed as follows —
plot_bar(ps.ng.tax_most_, x=”Family”, fill=”Family”, facet_grid = pre_post_stroke~Sex_age) + geom_bar(aes(), stat=”identity”, position=”stack”) +
scale_fill_manual(values = 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″)) + theme(axis.text = element_text(size = 5, colour=”black”), axis.text.x=element_blank(), axis.ticks=element_blank()) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=8))
“`
“`{r, echo=FALSE, warning=FALSE}
#MOVE_FROM_ABOVE: ## Bar plots in genus level
#MOVE_FROM_ABOVE: Regroup together pre vs post stroke samples and normalize number of reads in each group using median sequencing depth.
#plot_bar(ps.ng.tax_most_pre_post_stroke_, fill=”Genus”) + geom_bar(aes(), stat=”identity”, position=”stack”) +
#scale_fill_manual(values = 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″)) + theme(axis.text = element_text(size = theme.size, colour=”black”)) + theme(legend.position=”bottom”)
“`
\pagebreak
“`{r, echo=FALSE, warning=FALSE}
#MOVE_FROM_ABOVE: Use color according to genus. Do separate panels Stroke and Sex_age.
##– If existing replicates, to be processed as follows —
#plot_bar(ps.ng.tax_most_, x=”Genus”, fill=”Genus”, facet_grid = pre_post_stroke~Sex_age) + geom_bar(aes(), stat=”identity”, position=”stack”) +
#scale_fill_manual(values = 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″)) + theme(axis.text = element_text(size = 6, colour=”black”), axis.text.x=element_blank(), axis.ticks=element_blank()) + theme(legend.position=”bottom”) + guides(fill=guide_legend(nrow=18))
“`
\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
#FITTING2: CONSOLE:
#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.div_qiime <- read.csv("adiv_even.txt", sep="\t")
colnames(hmp.div_qiime) <- c("sam_name", "chao1", "observed_otus", "shannon", "PD_whole_tree")
row.names(hmp.div_qiime) <- hmp.div_qiime$sam_name
div.df <- merge(hmp.div_qiime, hmp.meta, by = "sam_name")
div.df2 <- div.df[, c("Group", "chao1", "shannon", "observed_otus", "PD_whole_tree")]
colnames(div.df2) <- c("Group", "Chao-1", "Shannon", "OTU", "Phylogenetic Diversity")
#colnames(div.df2)
options(max.print=999999)
#27 H47 830.5000 5.008482 319 10.60177
#FITTING4: if occuring "Computation failed in `stat_signif()`:not enough 'y' observations"
#means: the patient H47 contains only one sample, it should be removed for the statistical p-values calculations.
#delete H47(1)
#div.df2 <- div.df2[-c(3), ]
#div.df2 <- div.df2[-c(55,54, 45,40,39,27,26,25,1), ]
knitr::kable(div.df2) %>% kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
#https://uc-r.github.io/t_test
#We can perform the test with t.test and transform our data and we can also perform the nonparametric test with the wilcox.test function.
stat.test.Shannon <- compare_means(
Shannon ~ Group, data = div.df2,
method = "t.test"
)
knitr::kable(stat.test.Shannon) %>% kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
div_df_melt <- reshape2::melt(div.df2)
#head(div_df_melt)
#https://plot.ly/r/box-plots/#horizontal-boxplot
#http://www.sthda.com/english/wiki/print.php?id=177
#https://rpkgs.datanovia.com/ggpubr/reference/as_ggplot.html
#http://www.sthda.com/english/articles/24-ggpubr-publication-ready-plots/82-ggplot2-easy-way-to-change-graphical-parameters/
#https://plot.ly/r/box-plots/#horizontal-boxplot
#library("gridExtra")
#par(mfrow=c(4,1))
p <- ggboxplot(div_df_melt, x = "Group", y = "value",
facet.by = "variable",
scales = "free",
width = 0.5,
fill = "gray", legend= "right")
#ggpar(p, xlab = FALSE, ylab = FALSE)
lev <- levels(factor(div_df_melt$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, ...))
}
}
p2 <- p +
stat_compare_means(
method="t.test",
#comparisons = L.pairs, # L.pairs
comparisons = list(c("Group1", "Group2"), c("Group1", "Group3"), c("Group1", "Group4"), c("Group1", "Group6"), c("Group1", "Group8"), c("Group2", "Group5"),c("Group4", "Group5"),c("Group4", "Group6"),c("Group4", "Group7"),c("Group6", "Group7")),
label = "p.signif",
symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns")),
#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
#FITTING3: mkdir figures
ggsave("./figures/alpha_diversity_Group.png", device="png", height = 10, width = 12)
ggsave("./figures/alpha_diversity_Group.svg", device="svg", height = 10, width = 12)
p3 <- p +
stat_compare_means(
method="t.test",
#comparisons = L.pairs, # L.pairs
comparisons = list(c("Group2", "Group4"), c("Group2", "Group6"), c("Group4", "Group8"), c("Group6", "Group8")),
label = "p.signif",
symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns")),
#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
#FITTING3: mkdir figures
ggsave("./figures/alpha_diversity_Group2.png", device="png", height = 10, width = 12)
ggsave("./figures/alpha_diversity_Group2.svg", device="svg", height = 10, width = 12)
```
# Selected alpha diversity
```{r, echo=TRUE, warning=FALSE, fig.cap="Alpha diversity", out.width = '100%', fig.align= "center"}
knitr::include_graphics("./figures/alpha_diversity_Group2.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”))
“`
# Beta diversity
“`{r, echo=TRUE, warning=FALSE, fig.cap=”Beta diversity”, out.width = ‘100%’, fig.align= “center”}
#file:///home/jhuang/DATA/Data_Marius_16S/core_diversity_e42369/bdiv_even42369_Group/unweighted_unifrac_boxplots/Group_Stats.txt
beta_diversity_group_stats<-read.csv("unweighted_unifrac_boxplots_Group_Stats.txt",sep="\t")
knitr::kable(beta_diversity_group_stats) %>% kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
knitr::include_graphics(“./figures/PCoA.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.
## Group2 vs Group4
“`{r, echo=TRUE, warning=FALSE}
library(“DESeq2”)
#ALTERNATIVE using ps.ng.tax_most_copied: ps.ng.tax (40594) vs. ps.ng.tax_most_copied (166)
ps.ng.tax_sel <- ps.ng.tax
#FITTING5: correct the id of the group members, see FITTING6
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("8","9","10","12","13","14", "21","22","23","24","25","26","27","28")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group4")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
kable(sigtab) %>%
kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
#rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied))
write.xlsx(sigtab, file = “sigtab_Group2_vs_Group4.xlsx”)
#subv %in% v
### returns a vector TRUE FALSE
#is.element(subv, v)
### returns a vector TRUE FALSE
library(“ggplot2”)
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$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$Family), levels=names(x))
ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
#Error in checkForExperimentalReplicates(object, modelMatrix) :
# The design matrix has the same number of samples and coefficients to fit,
# so estimation of dispersion is not possible. Treating samples
# as replicates was deprecated in v1.20 and no longer supported since v1.22.
```
## Group2 vs Group6
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("8","9","10","12","13","14", "33","34","35","36","37","38","39","51")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group6")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 2.0
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
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))
```
## Group4 vs Group8
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("21","22","23","24","25","26","27","28", "47","48","49","50","52","53","55")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group8")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
kable(sigtab) %>%
kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
library(“ggplot2”)
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$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$Family), levels=names(x))
ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
```
## Group6 vs Group8
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("33","34","35","36","37","38","39","51", "47","48","49","50","52","53","55")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group8")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 0.05
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
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))
```
## Group1 vs Group5
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("1","2","5","6","7", "29","30","31","32")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group5")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 2.0
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
kable(sigtab) %>%
kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
library(“ggplot2”)
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$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$Family), levels=names(x))
ggplot(sigtab, aes(x=log2FoldChange, y=Family, color=Order)) + geom_point(aes(size=padj)) + scale_size_continuous(name="padj",range=c(8,4))+
theme(axis.text.x = element_text(angle = -25, hjust = 0, vjust=0.5))
```
## Group4 vs Group8
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("21","22","23","24","25","26","27","28", "47","48","49","50","52","53","55")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group8")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 2.0
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
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))
```
## Group3 vs Group7
```{r, echo=TRUE, warning=FALSE}
ps.ng.tax_sel <- ps.ng.tax
otu_table(ps.ng.tax_sel) <- otu_table(ps.ng.tax)[,c("15","16","17","18","19","20", "40","41","42","43","44","46")]
diagdds = phyloseq_to_deseq2(ps.ng.tax_sel, ~Group)
diagdds$Group <- relevel(diagdds$Group, "Group7")
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
resultsNames(diagdds)
res = results(diagdds, cooksCutoff = FALSE)
alpha = 2.0
sigtab = res[which(res$padj < alpha), ]
sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(ps.ng.tax_sel)[rownames(sigtab), ], "matrix"))
sigtab <- sigtab[rownames(sigtab) %in% rownames(tax_table(ps.ng.tax_most_copied)), ]
kable(sigtab) %>% kable_styling(bootstrap_options = c(“striped”, “hover”, “condensed”, “responsive”))
library(“ggplot2”)
theme_set(theme_bw())
scale_fill_discrete <- function(palname = "Set1", ...) {
scale_fill_brewer(palette = palname, ...)
}
x = tapply(sigtab$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))
```