Violin plot should allow to specify gene_symbols column in .var to use
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- Dominant language
- Python
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
Currently for most plots (where it makes sense) you can specify the column of .var which contains gene symbols. This doesn't seem to work for sc.pl.violin because
is not getting passed a gene_symbols argument when called from violin (that method does accept that argument). This should be an easy fix and make violin plot behave a bit more closely to the other plots. Happy to submit a PR.
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Research direction
Open scanpy/plotting/_anndata.py around line 727 and trace the sc.pl.violin call. Verify how the called method accepts gene_symbols and confirm that violin plots use the selected .var column when the option is provided.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100