Average Taxa Barplots

User Support
1

Taxonomy Abundance Bar-chart.

I am looking to create taxonomic barplots comparing the average taxonomic assignment of different categories eg. Male v Female, age categories, etc.

I have run the command:
qiime taxa barplot --i-table table-dada2.qza
–m-metadata-file metadata-file.txt
–o-visualization taxa-bar-plots.dada2.qzv

I then am able to visualise the barplot using:
qiime tools view taxa-bar-plots.dada2.qzv

I have 208 samples and I get a barplot containing 208 bars. I can group these bars by age or sex but am aiming to create a bar plot of the average of male and average of female (ie 2 bars).

I was looking to extract the file containing the relative abundance data so I could manipulate it and make some new plots in r.

I tried to convert the .qzv file into a .zip file and extract it but it didn’t seem to work. I followed the methodologies previously posted here but it doesn’t seem to work as I get a file of random numbers and characters out: How to convert .qzv file to .csv or .txt

QIIME 1 used to output these files as .biom or .txt files containing the OTU assignment and relative abundance for each sample. I am now using dada2 and ASVs in qiime2.

Maybe ASVs and OTUs are in the file differently?

Does anyone have any suggestion about whether this is the correct approach or whether I am missing something?

Thanks.

2

Use qiime feature-table group to group samples by a sample metadata category (sex). Then run barplot and you will have 2 columns displaying the average relative abundance across both groups.

Hope that helps!

2 Likes
3

Thanks, that seems to have worked. Just need to work out how to extract the .csv files now.
Thank you!

1 Like
4

The barplot visualization has a "download as CSV" (or maybe TSV) option in the top-left corner.

1 Like
5

Thanks - working now, was a problem with the computer before which is why they weren’t extracting.

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