UMAP ignores n_components when initial position is paga
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Description
When I run sc.tl.umap with the standard setting, init_pos = 'spectral', I get whatever number of components I specified via n_components. However, when I use init_pos = 'paga' for a paga representation I computed before, I always only get 2 components, no matter how I set n_components. From looking at the code, I don't understand why this is happening. Is there a principal reason for this, or is this a bug? Thanks!
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Research direction
Start at sc.tl.umap and compare init_pos='paga' with init_pos='spectral' while varying n_components. Reproduce the dimensionality mismatch and verify that the PAGA initialization path produces the requested number of components.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100