Availability and/or Export of data used for boxplots (balance-taxonomy)

User Support
1

Hello there,

**tl;dr: ** Is there a possibility to export the data which creates the Boxplots during balance-taxonomy?

I'm using gneiss for some community analyses at the moment.
Therefore i want to correlate more than two factors (e.g. different tree species against control and themselves).
As fas as i know, gneiss is only capable of plotting boxplots (balance-taxonomy) of two factors.

Is there a possibility to export the data which creates the Boxplots during balance-taxonomy?
I tried to use an “–output-dir” instead of the visualisation and to export the qzv in generel. Both doesn’t work for now.

I saw that sometimes there is the possibility to download a.csv-file directly from the qiime2viewer.
Would be really nice this feature could also be added sometimes in the future.

best regards
Chris

2

Hey Chris,

According to the documentation for balance-taxonomy, I'm pretty sure --output-dir should do exactly this...

What version of qiime are you using?

Have you tried exporting or extracting the .qzv file?

Let me know what you find,
Colin

3

Hey Colin,

thanks for your reply.

I'm using QIIME 2 version: 2017.12.1 (q2cli version: 2017.12.0) at the moment.

i tried the --output-dir variable and it just generated a folder with the .qzv-file.

I also tried to qiime tools extract and this worked temporary. I'll take a further look at the extracted files and if they provide the information i need.

Thanks for your input, i only tried export and this doesn't worked.

Best regards
Chris

5

These are just standard q2 archives -- I think @ebolyen and @thermokarst could elaborate more on that.

Note that a q2 archive is really just a zip file. A sure fire way to open a zip file is just

tar -zxvf <your-file-name.qzv>
6

@mortonjt, I think @Tjelve is more interested in getting the summaries that define each of these boxplots, or maybe the original distributions themselves. I don't think this data is readily available in a .qza and it doesn't seem like the .qzv provides it as a csv/tsv download either.

How would we go about getting the pre-plot info from balance-taxonomy? Are there some functions in gneiss we could call separately?

7

I don't think that information is accessible. Underneath the hood, we are just using seaborn (see function here).

However, seaborn is a little customizable, so it is possible to use the Python function to do more custom visualization (i.e. nested box plots).

9

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