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 the actual visual heatmap. Thanks
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…
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 these goodies inside. Is there an official write up of that?
As for the contents of the extracted viz, I don’t think you’ll find any TSVs or CSVs for this particular visualization (although it sounds like maybe you found an alternative path forward, based on your reply above?). You marked a “solution”, which implies that your original request has been resolved. If not, please clarify. The reason I shared the export/extract tutorial is that it is written up in more detail, compared to @colinbrislawn’s “hack” that you shared.
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. In the case of the heatmap visualization, the raw data are not stored in there, only the image I believe. Let me see if I can get you close to what you want:
You can use export to export your feature table (the one used as input to heatmap) as a biom, then convert the biom to a TSV using biom convert --to-tsv.
Exporting the feature table would not replicate this sorting. You could just export and either manually sort (if the table is small!) or supplement the unsorted table.
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?
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 a hindrance to most users, though (this would increase runtime and create another file to clutter up the workspace!). I have opened an issue to track this here but my feeling right now is that this will be a low priority unless if we get more demand for this (this is the first request we’ve had) — contributions are always welcome!