Feature-table filter-features keep samples for heatmap


I have run Indicator analysis in R and would like to create a heat map using feature-table heatmap with a feature table that contains only the indicator sequence variants. I tried running feature-table filter-features (keeping the indicator sequence variants) but the output table has does not contain all my samples. Is there a way to keep all samples in the output table? If not, is there a way to specify which sequence variants to include in the heatmap via feature-table heatmap?

Thank you,

filter-features should not drop samples, only features. Are you sure the input table contained all samples? Please run qiime feature-table summarize on the input and output tables to check — if you are still having trouble, please post those QZVs, the filtering command that you used, and your indicator species list here so we can help troubleshoot.

No — filtering must be performed upstream.

I hope that helps!

Thank you Nicholas for your quick response. I've attached my input and output table summaries (created via 'qiime feature-table summarize' and my indicator species list.

The filtering command I used:
$ qiime feature-table filter-features
--i-table rarefied_table_e1185_Acropora_millepora_remove_unhealthy.qza
--o-filtered-table rarefied_table_e1185_Acropora_millepora_remove_unhealthy-INDICATOR-TAXA-ONLY
--m-metadata-file Indicispecies_Acropora_list.txt

The input table has 66 samples and the output table has 23 samples. qiime feature-table filter-features says "Any samples
with a frequency of zero after feature filtering will also be removed." Some of these indicators likely have a frequency of zero in some samples (making them good "indicator taxa" of my treatment groups).

Indicispecies_Acropora_list.txt (1018 Bytes)
summarize_rarefied_table_e1185_Acropora_millepora_remove_unhealthy.qzv (427.6 KB)
summarize_rarefied_table_e1185_Acropora_millepora_remove_unhealthy-INDICATOR-TAXA-ONLY.qzv (381.9 KB)

I apologize for multiple correspondences but I discovered that some of the features have an extra character "X" at the beginning of the feature id. I corrected this and ran the following filtering command:

$ qiime feature-table filter-features
–i-table rarefied_table_e1185_Acropora_millepora_remove_unhealthy.qza
–o-filtered-table rarefied_table_e1185_Acropora_millepora_remove_unhealthy-INDICATOR-TAXA-ONLY
–m-metadata-file Indicispecies_Acropora_list_remove-added-character.txt

Unfortunately, I still have missing samples (see attached visualization).

summarize_rarefied_table_e1185_Acropora_millepora_remove_unhealthy-INDICATOR-TAXA-ONLY_extra_character_removed.qzv (378.4 KB)
Indicispecies_Acropora_list_remove-added-character.txt (997 Bytes)

I apologize — I was mistaken and you are correct. I have raised an issue to address this (e.g., make dropping empty samples optional) and I agree this could be bad behavior in some circumstances.

For now, I'm not sure there is a great workaround that is 100% in :qiime2:... the best approach is probably to export your feature table and generate something in R, where you can have more control to customize this plot. Sorry I don't have a better solution at the moment!

Thanks for raising this issue!

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