Heatmap generation with clustered groups

[M_F (Meriem)]

Hi,

I would like to generate a heatmap showing the clustered groups (T2D, H, OB, and T2D_CV). However, when I use the following command lines, the resulting heatmap is generated for individual participants rather than for the predefined groups.

qiime taxa collapse
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-level 6
--o-collapsed-table collapsed-table-l6.qza

qiime feature-table heatmap
--i-table
--m-sample-metadata-file
--m-sample-metadata-column Disease
--p-metric correlation
--p-method complete
--o-visualization

I contacted you previously regarding this issue, and you kindly advised me to refer to the following post.

Error when trying to group heatmap

Hi, I think I have same problem as @SetaPark had. But, I don't think I am understanding the suggested solution. I am trying to average my samples by group and visualize the group average using heat map. [Myungran heat] The heatmap above list all the individual samples But I would like to represent by group average (like what @SetaPark explained with the drawing above but in heatmap not in taxabarplot). I have 22 samples and the are grouped by their fermentation periods. editedmeta.txt (1…

I would like to inform you that the suggested approach does not resolve the issue in QIIME 2 Amplicon 2025.4. My metadata file is in TSV format and includes all participants along with their corresponding group assignments.

Could you please provide the appropriate QIIME 2 command lines to:

1. Cluster samples according to their respective groups (T2D, H, OB, and T2D_CV), and

2. Generate a heatmap that displays the abundance patterns at the group level rather than for individual participants?

Best

[cherman2 (Chloe Herman)]

Hi @M_F,
qiime taxa collapse groups your features by taxonomic level, I believe you want to group your samples?

I would use qiime feature-table group and then run the heatmap on the resulting table. feature-table - Microbiome marker gene analysis with QIIME 2.

Something that is really important here is that you must make a new metadata that has your groups as the sample ids or else qiime2 will fail like in that linked forum post you sent.

Hope this helps!