add restrict_to to sc.pl.umap function?
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Description
Hello,
In some cases, I need to visualize clustering results (categorical) on UMAP for each batch.
I know sc.pl.umap(adata[adata.obs['batch] == 'batch1], color = 'louvain') is a solution. However, other cells are missing. I think the other cells colored by grey as background should be a better way.
I notice that sc.pl.umap(adata, color = 'batch', groups = ['batch1'] ) can retain other cells as grey, though sometimes cells were submerged in the bottom layer (I used reoder_categories to bypass this issue). But, color and groups must be correspondence!
Is there any way to fulfill my needs in Scanpy if I missed something.
Or, could the authors add a parameters, such as restrict_to in sc.tl.louvain, to implement this function: ① liberate strong associations between color and groups, and ② add support for ordering categorical variable
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Research direction
Start by reviewing the sc.pl.umap entry point and its handling of color, groups, categorical ordering, and background cells. Clarify whether the desired behavior is an independent restriction parameter, categorical ordering support, or both; done should be a documented API behavior with coverage for the requested batch visualization.
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Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100