biocore / biocore/mmvec

bug: paired-heatmap top-k-microbes fails when top microbes are not found in ranks

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Dominant language
Python
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Description

Error reported in [QIIME 2 forum](https://forum.qiime2.org/t/error-in-q2-mmvec-and-some-other-question/12562)

The issue is at these lines:
https://github.com/biocore/mmvec/blob/ec082d25be946971d203d96e77504aaaa3157cfc/mmvec/heatmap.py#L199-L201

This results in a KeyError if any of the features (microbes) are missing from the ranks table.

either those lines should be amended to grab only features that are present in ranks, or better yet ranks and microbes_table should be subsetted to keep the intersection somewhere before this line:
https://github.com/biocore/mmvec/blob/ec082d25be946971d203d96e77504aaaa3157cfc/mmvec/heatmap.py#L175

Contributor guide

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Research direction

Start in mmvec/heatmap.py at lines 175 and 199-201, then trace how the ranks table and microbes table are selected for paired-heatmap top-k-microbes. Reproduce the reported case with microbes missing from ranks and confirm that the command completes without a KeyError while retaining only valid features.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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