Export hetamap to tsv

[shira]

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

[timanix (Timur Yergaliyev)]

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.

[shira]

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…

How to convert .qzv file to .csv or .txt

Good morning Kim, Great question! The Qiime 2 files like .qza and .qzv are just .zip archives. So to open one up, you can simply rename it as a .zip file, then extract it. mv shannon_vector.qzv shannon_vector.zip unzip shannon_vector.zip Of course, you could also rename it in the folder and simply double-click to extract. That’s probably easier than the command line Once you have extracted it, you can open up the folder and find the Shannon vectors inside. Let me know if thi…

[thermokarst]

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/

[shira]

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?

[thermokarst]

@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 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.

[shira]

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

[Nicholas_Bokulich]

@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. 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:

@shira

I would like to export a heatmap to a tsv format.

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.

@shira

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.

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.

[shira]

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?

[Nicholas_Bokulich]

@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 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!

Thanks @shira !

[gibsramen (Gibraan Rahman)]

Hi @shira

@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 feature-table heatmap uses seaborn.clustermap under the hood.

The underlying “clustered” data can be retrieved using the data2d property of the clustermap. So if you have a clustermap plotted like this:

g = sns.clustermap(...)

g.data2d would return a DataFrame “ordered” by the clustermap rows/columns.

This may require you to plot the clustermap manually, as I am not super familiar with Qiime2’s visualization data architecture.