Qurro: Export numerator - denominator list

Hello,
An auto-selection value of 5% at a specific axis results in considerabl deifferences in the log-ratio between different sample groups and displays the interesting list of taxa in the nominator and denominator section of qurro plots. Is there any possibility to export the nominator and denominator list from the qurro plot visualisation?
Best regards,

2 Likes

pinging @fedarko… thank you both!

1 Like

Hi @arwqiime,

There isn’t an easy way to do this right now, sorry – I’ve had this on my TODO list for Qurro for a while now (the relevant issue is here). Hopefully we’ll be able to get this sort of functionality implemented soon.

In the meantime, if you just want to check out the IDs of the top- / bottom- ranked features for a given ranking, you can always inspect the rankings outside of Qurro – for example, by loading the corresponding QZA through the QIIME 2 Artifact API, then going from there to a Pandas DataFrame representation of the rankings (from which you can use methods like .nlargest() or .nsmallest() to retrieve the extremely ranked features for a given ranking).

3 Likes

Hi @arwqiime

I think I have a really hacky solution that might address your needs.

When you’re on the webpage with the Qurro visualization, you can “inspect element” (on Chrome) and see all the constituent parts of the webpage. If you dig deep enough into the datatables you should find all the features you are looking for. You should be able to copy the element containing them and then paste into a document on which you can perform some text searching to find the IDs.

I’ve attached a screenshot of where this appears on my end.

Super cumbersome and possibly unstable with future Qurro updates but I hope it helps you out in the short-term.

EDIT: I think you can right-click the <tbody> tag and copy the whole element which I think should give you all the rows.

2 Likes

@fedarko, @gibsramen Hi. thanks a lot for your comments and pointing me to some workarounds.
Actually, I select the table content and copy it via the clipboard, which works but it is not very conveniant (and error-prone, if you do not select the entire table for some reasons).
If a ‘copy-to-clipboard’ button wold be easier to implement compared to a csv exporter, this would be sufficient.

Thanks again!

1 Like

@arwqiime The copy-to-clipboard solution is a cool idea, thanks! In terms of effort needed to implement things, I think that would be a similar amount of work as just exporting a TSV file (like is already done for the sample plot data).

Your question inspired me to get some work done on the selected feature list export – here’s a tentative screenshot of what the interface will look like. Out of curiosity, what sort of output file would be most useful for you? I’m thinking along the lines of a simple TSV file formatted like

"Feature ID" [tab] Log_Ratio_Classification
ASV1         [tab] Numerator
ASV2         [tab] Denominator
ASV3         [tab] Numerator
ASV4         [tab] Both

but if you’d prefer something else, just let me know and I may be able to sort it out. (That being said I can’t promise I’ll get this finished soon – things are getting a bit busy over here…)

edit: I bit the bullet and got a draft version of this functionality implemented over in https://github.com/fedarko/qurro/. The new functionality in this version isn’t tested yet (this version of Qurro should be treated as “experimental” for now), but if you want to try it out you should be able to install it using pip install git+https://github.com/fedarko/qurro.git :slight_smile:

2 Likes

@fedarko

Yes, a TSV export (including the colum headers) would be just fine!
Thanks!

3 Likes

Yes, a TSV export (including the colum headers) would be just fine!

Ok, version 0.6.0 of Qurro (out now!) has support for this! Hope this is useful.

Hi @fedarko, thank you for the export function! Is it correct that only the ‘feature’ and the ‘log ratio classification’ columns are exported, but not the PCA values for axis1/2/3, the taxon, and the confidence column? Would it be possible to get the entire table?

Best regards!

Hi @arwqiime, yes as of right now just those two columns are exported. It’d be possible to export all of the columns, but this would take some extra work – I’ve created an issue to keep track of this here.

I probably won’t be able to get to that for a while since things are pretty busy over here, sorry.