Sample-classifier heatmap error empty table

I am having an issue trying to obtain get the sample-classifier heatmap output annotated with taxonomy intead of feature IDs.

I tried collapsing the feature table and using this collapsed table as input but it does not work.

The command I am running is this one:
qiime sample-classifier heatmap /
–i-table collapsed-table-species-level.qza /
–i-importance sample-classifier-prediction-results/feature_importance.qza / --m-metadata-file metadata-comb-rep1-rep2.tsv /
–m-metadata-column Diagnostic /
–p-group-samples /
–p-feature-count 100 /
–o-heatmap heatmap.qzv /
–o-filtered-table filtered_table_taxonomy.qza

And then the output is this:
Plugin error from sample-classifier:

Cannot group an empty table.

Debug info has been saved to /tmp/qiime2-q2cli-err-dzsqdsrz.log

Any ideas what might be going wrong?



you need to use the same feature table that you provided as input to classify-samples. If you collapse your feature table, the feature IDs no longer match what is in the importances file.

Good luck!

Hi @Nicholas_Bokulich

Thnaks for your input. However, I wanted the heatmap to show the actual taxonomy IDs and not the feature IDs. I read somewhere else in the forum that I needed to collapse the feature table and then use that table with sample-classifier heatmap.

Is this correct?


That is a solution for feature-classifier heatmap and perhaps what you read. For sample-classifier heatmap see this solution: