I was wondering if there is a way to easily get the percent relative abundance from the
qiime taxa barplot ? The
taxa-barplot.qzv itself shows the percent relative abundance, but when I download the csv file it is in absolute abundance. Would be a nice additional feature
In the upper-left corner of taxa-barplot there is a series of download buttons. You can download as a CSV by clicking the button, as shown in this screenshot. These buttons were added in a recent QIIME 2 release, so if you do not see them then simply re-run the command used to generate the barplots with the latest version of QIIME 2 and voila.
I hope that helps. If that's not what you are looking for, please let us know!
Thank you for the quick response. I am able to download the csv file as recommended in the screen shot; however, I was wondering how I can get a similar csv file that has the relative abundances (or percent relative abundance ) as shown on the actual bar plot image. Right now when I download the csv file, as you mentioned, I get counts. I have attached the example csv file (converted to txt).
level-5.txt (1.7 KB)
@pjtorres I apologize, I misunderstood your initial post — I see now that the csv you describe is coming from that same download.
I have created a feature request for this issue here — though the developer of that plugin may disagree that this is an issue (as absolute abundances are consistent with the input data).
For now, you can instead generate your desired output by using
taxa collapse to collapse your feature table to the taxonomic level of interest, convert to relative abundances with
feature-table relative-abundance, and then export the table. Would that produce your desired output?
It definitely works this way. It would be nice to have the option to directly download it from the bar plot figure similar to the current way with the counts - just a thought. Thank you @Nicholas_Bokulich!
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