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Mapping new ps_* objects to the old ps.ng.tax* objects (and overwrite notes)
| ps_* object | What it contains | Old R-script equivalent (ps.ng.tax*) | Overwrite notes for old object(s) | Taxonomic composition | Alpha diversity | Beta diversity | DESeq2 differential abundance |
|---|---|---|---|---|---|---|---|
ps_raw |
Raw imported phyloseq object (integer counts; as imported) | (no direct equivalent) | — | ❌ | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_base |
ps_raw + taxonomy + sample metadata aligned (still raw counts) |
(closest to) ps.ng.tax before overwrite |
Old ps.ng.tax BEFORE overwrite: integer count table (absolute abundance). |
❌ | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_pruned |
Optional subset of ps_base (e.g., remove unwanted samples by ID/pattern); still raw counts |
(subset of) ps.ng.tax before overwrite |
Old ps.ng.tax BEFORE overwrite: same as above, but without any sample subsetting unless you did it. |
❌ | ❌ | ❌ | ⚠️ only if you also apply low-depth filtering |
ps_filt |
Filtered samples (low-depth samples removed) + taxa with nonzero totals; absolute counts | ps.ng.tax before overwrite (but with explicit low-depth filtering) |
Old ps.ng.tax BEFORE overwrite: raw integer counts; new ps_filt is the “cleaned” version after sample-depth QC. |
✅ as a starting point (but plot on ps_rel) |
✅ as input to rarefaction | ✅ as input to rarefaction | ✅ as input to ps_deseq |
ps_rel |
Relative abundance (compositional) computed from ps_filt |
ps.ng.tax_rel (conceptually) |
In the old script, ps.ng.tax_rel is “relative abundance of ps.ng.tax”, but its meaning depends on whether it was computed before or after ps.ng.tax was overwritten. |
✅ primary | ❌ | ❌ | ❌ |
ps_abund |
Absolute counts after “plotting taxa filter” (e.g., mean rel. abundance > 0.1%), derived from ps_filt via ps_rel |
ps.ng.tax_abund |
Old ps.ng.tax_abund was created by filtering taxa using mean relative abundance (> 0.001) and then pruning counts. |
✅ (if you want cleaner plots) | ❌ | ❌ | ❌ (not recommended) |
ps_abund_rel |
Relative abundance computed from ps_abund (filtered taxa set) |
ps.ng.tax_abund_rel |
Old ps.ng.tax_abund_rel was relative abundance of the filtered-taxa object. |
✅ (clean composition plots) | ❌ | ❌ | ❌ |
ps_rarefied |
Rarefied counts from ps_filt (even depth) |
ps.ng.tax after overwrite |
Old ps.ng.tax was overwritten 1× by rarefy_even_depth(ps.ng.tax, sample.size = 41764) → after this, ps.ng.tax no longer meant raw counts; it meant rarefied counts. |
❌ | ✅ primary | ✅ primary | ❌ |
ps_deseq |
Non-rarefied integer counts from ps_filt + optional count-based taxon prefilter (e.g., total ≥ 10) |
(no direct equivalent) | Old ps.ng.tax_abund is not a good DESeq2 analogue because it used a mean-relative-abundance filter; ps_deseq uses count-based prefiltering (optional) and keeps integer counts. |
❌ | ❌ | ❌ | ✅ primary |
Overwrite summary (old script):
ps.ng.taxwas overwritten 1 time:- Before overwrite:
ps.ng.tax= absolute abundance (raw integer counts). - After overwrite:
ps.ng.tax= rarefied counts, produced byrarefy_even_depth(ps.ng.tax, sample.size = 41764).
- Before overwrite:
| ps_* object | What it contains | Taxonomic composition | Alpha diversity | Beta diversity | DESeq2 differential abundance |
|---|---|---|---|---|---|
ps_raw |
Raw imported phyloseq object (integer counts; as imported) | ❌ (not recommended directly) | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_base |
ps_raw + taxonomy + sample metadata aligned (still raw counts) |
❌ | ❌ | ❌ | ⚠️ only if you also apply sample filtering first |
ps_pruned |
Optional subset of ps_base (e.g., remove unwanted samples by ID/pattern); still raw counts |
❌ | ❌ | ❌ | ⚠️ only if you also apply low-depth filtering |
ps_filt |
Filtered samples (low-depth samples removed) + taxa with nonzero totals; absolute counts | ✅ as a starting point (but plot on ps_rel) |
✅ as the input to rarefaction | ✅ as the input to rarefaction | ✅ as the input to ps_deseq |
ps_rel |
Relative abundance (compositional) computed from ps_filt |
✅ primary | ❌ | ❌ | ❌ |
ps_abund |
Absolute counts after “plotting taxa filter” (e.g., mean rel. abundance > 0.1%), derived from ps_filt via ps_rel |
✅ (if you want cleaner plots) | ❌ | ❌ | ❌ (not recommended) |
ps_abund_rel |
Relative abundance computed from ps_abund (filtered taxa set) |
✅ (clean composition plots) | ❌ | ❌ | ❌ |
ps_rarefied |
Rarefied counts from ps_filt (even depth) |
❌ | ✅ primary | ✅ primary | ❌ |
ps_deseq |
Non-rarefied integer counts from ps_filt + optional count-based taxon prefilter (e.g., total ≥ 10) |
❌ | ❌ | ❌ | ✅ primary |