paga inconsistency with plotting functions
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- Dominant language
- Python
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Description
Functions like sc.tl.umap support initialization with group centroid coordinates derived from sc.pl.paga. Unfortunately pl.paga only returns 2D coordinates, whereas embedding support n_components >2. I found that if init_pos is set to paga, the number of components is always set to 2. I understand the behavior, but wouldn’t it be more consistent if paga could be return arbitrary sized coordinates?
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Research direction
Trace the sc.pl.paga coordinate generation and sc.tl.umap handling of init_pos and n_components. Check where PAGA coordinates are constrained to two dimensions and how UMAP consumes them. Done means PAGA can provide coordinates matching the requested dimensionality and initialization no longer forces n_components to 2; add or update focused tests for this behavior.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100