This topic may seem odd, and I haven't found reference to this in the forum - so here goes: I would like to export a heatmap to a tsv format. More specifically, the features are clustered and I would like to replicate the order of the clustered features, to use as a supplementary table alongside th…

Hi! I don't remember about heatmaps, but if you will open a corresponding .qzv file as archive and navigate to 'data' subfolder, you will find all necessary files, including .tsv or .csv tables.

Awesome! Many thanks @timanix for this neat method. I did have to lookup how to do it, and found it here, works great, just like exporting, but easier :slightly_smiling_face: *Unfortunately this did not solve my problem though... [image] How to convert .qzv file to .csv or .txt Us…

Hi @shira ! Glad you found that post, but for the sake of demonstration, I'll point you towards the "official" QIIME 2 solution: https://docs.qiime2.org/2020.2/tutorials/exporting/ :qiime2:

Thanks @thermokarst , but the tutorial you cite talks about exporting, but actually does not solve my original problem which was the need to obtain the table containing the clustered heatmap data. I could not find any mention of this super useful 'trick' of opening a QZV file as a ZIP and finding all…

[image] shira: Is there an official write up of that? Yes, but not in a tutorial: https://dev.qiime2.org/latest/storing-data/ See this section of the tutorial I sent earlier for details on "extracting": https://docs.qiime2.org/2020.2/tutorials/exporting/#exporting-versus-extracting As for…

Thanks @thermokarst - you are right of course! The table I was looking for was not among the files after all :frowning: I unmarked the "solution" button - but what is the solution?

[image] shira: I unmarked the “solution” button - but what is the solution? I don't think there is a solution that gets you exactly what you want. @timanix and @thermokarst provided details on the way to export/extract data from any QZA/QZV, but that only works if the data are stored in there…

Thanks @Nicholas_Bokulich . That's too bad, it would be quite useful, for publication purposes. As far as I understand, in R you can easily get the sorted row names back, perhaps this should be added to the exported data in a QIIME heatmap as well?

[image] shira: as I understand, in R you can easily get the sorted row names back, perhaps this should be added to the exported data in a QIIME heatmap as well? Yes, this can also be done using the python module that QIIME 2 uses to make this heatmap. I am not sure if this would be useful or …

Hi @shira [image] shira: but actually does not solve my original problem which was the need to obtain the table containing the clustered heatmap data This is something I've done in Python though it was with mmvec results rather than a feature-table heatmap. My understanding is that qiime fea…

Export hetamap to tsv

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shira April 14, 2020, 12:39pm 3

Awesome! Many thanks @timanix for this neat method.
I did have to lookup how to do it, and found it here, works great, just like exporting, but easier
*Unfortunately this did not solve my problem though...