Add support for passing boolean columns in .obs when plotting clustermap or dendrogram.
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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?
Hey,
currently, when trying to use plotting functions that require categorical obs columns (for example sc.pl.clustermap obs_keys parameter), but one passes a boolean column key in .obs, scanpy will raise an error (or pandas does but the origin is in scanpy's codebase): AttributeError: Can only use .cat accessor with a 'category' dtype.
Would it be possible to let the passed key be from a column of dtype bool as well? Are there any downsides? Happy to provide more detail if needed.
Contributor guide
First steps
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Research direction
Start by tracing how sc.pl.clustermap and dendrogram process obs_keys and categorical columns. Reproduce the AttributeError with a boolean .obs column, then identify the existing plotting tests or entry points that cover categorical inputs. Done means boolean columns are accepted for these plotting paths without breaking categorical handling.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100