Heatmap and the legend

User Support
1

Hi everyone,

I am trying to personalize the heatmap I have generated using:

qiime feature-table heatmap
--i-table collapsed-table-lvl7-dada2-LB18_31_1-filtered-edited.qza
--m-metadata-file metadata-LB18_31-L1.csv
--m-metadata-column Description
--p-metric braycurtis
--p-cluster features
--output-dir heatmap

visualization.qzv (872.8 KB)
metadata-LB18_31.csv (5.2 KB)

As mentioned here already in this forum I could modify taxonomic names in biom files exported to tsv. However I don't know how to remove the names of my samples.

Here I explain:

  • SampleID - working ID of the sample, I don't need to have it on the plot, each file generated from sequencer had in individual name starting LB17_16...
  • Decription - initials of a patient - the sample name I am interested in
  • Group - patients grouped by healthy / ill etc condition

What I need on the heatmap is to have patients description and a group. Yet, I still get sampleID - how to remove it?

Do you have any suggestions?
I would be very grateful also for any other suggestions for such a heatmap to look more pro.

Thank you for any help.

3

Hey hey @Jo_mee!

Create a new metadata column in your sample metadata file with this combined information, then specify the new column when generating your heatmap! :fire: :world_map:

5

Dear @thermokarst,

I did as you suggested - combined Group_Description in one column of my metadata file and then used it in the command. It worked!
But...
What I got was the combined Group AND Description and additionally there was "LB17-16..." (the #SampleID from the first column of metadata). I don't what to have it.

Please, help me to remove it!

7

Hi @Jo_mee

You won't be able to remove it as-is using this visualization - if you need to you can download the SVG and edit in another tool.

Another option is to "group" your table by this new metadata column, the plot the heatmap of the grouped table. The labels will look like how you want, but, some of your samples might be collapsed together (this depends on if there are any duplicates in the metadata column or not).