How to generate a differential abundance graph in QIIME2 with taxon as label instead of Feature ID/Sequence


I am currently busy with a 16S microbiome analysis and doing the differential abundance with ANCOM and ANCOMBC - as my version of qiime2 does not have aldex2 as an option. I am able to generate the graphs with the following code:

#ANCOM-BC single formula
qiime composition ancombc
--i-table SCZ_table.qza
--m-metadata-file merged-data.tsv
--m-metadata-file CR_sample_data.txt
--p-formula Status
--p-p-adj-method 'BH'
--o-differentials SCZ_DiffAbun_status.qza


#ANCOM-BC - tabular
qiime composition tabulate
--i-data SCZ_DiffAbun_stat+sex+currS.qza
--o-visualization SCZ_DiffAbun_stat+sex+currS_tab.qzv

qiime composition tabulate
--i-data SCZ_DiffAbun_status.qza
--o-visualization SCZ_DiffAbun_status_tab.qzv

#Differential abundance bar plots - da-barplot
qiime composition da-barplot
--i-data SCZ_DiffAbun_stat+sex+currS.qza
--o-visualization SCZ_DiffAbun_stat+sex+currS_bp.qzv

qiime composition da-barplot
--i-data SCZ_DiffAbun_status.qza
--o-visualization SCZ_DiffAbun_status_bp.qzv

However, the label on the y-axis is given as the taxa sequence (or Feature ID) and not the taxon name (or Genus name). I have been trying to find how to do but can seem to figure it out.

I tried transposing my FeatureTable[Frequency] to merge it with rep-seqs.qza and taxonomy.qza, but I think I need to find a way to have the Feature ID, taxon name and sample ID in one file for metadata. And I am not sure what to put together.

Hello Carlien,

Welcome to the forums :qiime2:

This is a great idea! It's being discussed in this GitHub issue but it looks like it has not been implemented yet.

You can follow this thread or that issue for further updates.


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