Heatmap - qiime feature-table heatmap

Hello :slight_smile:

I have created Heatmap using ‘qiime feature-table heatmap’ command.
I chose metadata-category, but the heatmap I received included the category I chose but not in the right order - all groups from this category are mix.

I have checked the table by converting it to tsv - and all samples are well organized there.

please help :slight_smile:


Hi @Adi,
Please see this post. Specifically, set --p-cluster to “features” to disable sample clustering and then your groups should be ordered correctly.

I hope that helps!

1 Like

Hi @Nicholas_Bokulich
Thanks alot!
I tried to set --p-cluster to “features”. the groups ordered correctly, but now instead of having the taxa name I got the features name.

Hi @Adi,
Good to hear that solved the ordering issue!

That’s a bit mysterious… are you inputting the same feature table? The feature IDs should be the same as they are in the feature table. So if you use a feature table containing OTUs/sequence variants, the labels will be those feature IDs. If you collapse by taxonomy, then your features will be taxa instead (e.g., genera, species). Is that what you are looking for?

I hope that helps! :sunflower:


Thanks a lot, probably I chose the wrong table…now all good :slight_smile:

Is there a way to show only the significant taxon in the heatmap?


Hi @Adi,

The only way to do this would be to filter your feature table to only contain significant features (or any features you want to display for that matter). This is a fairly straightforward process — input a list of significant features (such as would be output from ANCOM or another differential abundance method as a TSV file) as a metadata file to filter-features. Only features found in that list will be retained in the output.

I hope that helps!


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.