Export percentage of taxa-bar-plots.qzv to csv

[Yanfei-Geng]

when i export data from taxa-bar-plots.qzv to csv, how to export the percentage information? thx.!

taxa-bar-plots|690x157

[thermokarst]

Hi @Yanfei-Geng! Exposing this CSV download as relative abundances is on our radar, but we haven’t gotten to it just yet. You can always compute these values yourself using the absolute values available in the CSV. Stay tuned, we will update this post when that feature becomes available (although right now we don’t have a good ETA for when that will happen). Thanks!

[pjtorres (Pedro J. Torres)]

Hey @Yanfei-Geng,

I have had this issue before when needing percentages. I wrote this script to convert the csv file which you download from the taxa-bar-plots.qzv into percent abundance. Hope this helps!

[Jaroslaw_Grzadziel (Jarosław Grządziel)]

Another question in this matter is, if there is any possibility to export aggregated counts of each taxa ?
Currently after exporting, one need to aggregate the same taxa using for example R (phyloseq) while it would be more useful to use qiime2 instead.
Thanks in advice

[Yanfei-Geng]

thank you very much, 谢谢 xiexie.

[thermokarst]

Hi @Jaroslaw_Grzadziel - how about something like the following:

$ qiime taxa collapse \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 6
  --o-collapsed-table genus-table.qza
$ qiime feature-table summarize \
  --i-table genus-table.qza \
  --o-visualization genus-table.qzv

[Jaroslaw_Grzadziel (Jarosław Grządziel)]

Hi @thermokarst, it totally solved my problem !
Thank you, maybe this step should be placed somewhere inside a tutorial ?

[thermokarst]

Hi @Jaroslaw_Grzadziel!

We have an example of collapsing a feature table in the Moving Pictures tutorial!

[Jaroslaw_Grzadziel (Jarosław Grządziel)]

@thermokarst thank you and sorry for my mistake