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

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1

I have performed ANCOM-BC to find differential abundant taxa between groups using this code:

qiime composition ancombc
--i-table output/id-filtered-table.qza
--m-metadata-file metadata.tsv
--p-formula province
--p-p-adj-method holm
--p-reference-levels "province::W"
--o-differentials output/differentials.qza

qiime composition da-barplot
--i-data output/differentials.qza
--p-significance-threshold 0.05
--p-significance-label q_val
--p-level-delimiter ';'
--o-visualization output/differentials_id_filtered.qzv

I am able to generate plots, but the labels on the y-axis are the taxa sequence (or Feature ID) and not the taxon name.

I have tried to add taxonomy using

qiime metadata tabulate
--m-input-file output/differentials.qza
--m-input-file output/taxonomy.qza
--o-visualization output/differentials-with-taxonomy.qzv

but this doesn't work as there was an issue with viewing the artifact 'output/differentials.qza' as QIIME 2 Metadata ( Artifacts with type FeatureData[DifferentialAbundance] cannot be viewed as QIIME 2 metadata).

I can only have the taxa if I run qiime taxa collapse first at a certain level, but this does not generate exactly the same results (due to multiple testing correction?).

I know this question has been asked before, but I could not find the final answer.

Thanks,

2

Hi @dr_hulk,
This is functionality that is in the works for a future release of QIIME2. You can follow the github issue here. The work around currently is to run qiime taxa collapse, you can find more details here. Hopefully that gets you closer to your desired outcome while we work on the functionality!
--Hannah

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