pl.umap/tsne/draw_graph colored by principal component or diffusion component
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Description
Dear scanpy developers,
I would like to color my tsnes, umaps and graph layouts by specific principal components or diffusion components. Any chance you could add an option to use columns from obsm objects as colors for these plots? (Or maybe that's already possible and I missed it...?)
Thanks for your help.
Best,
Lisa
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the plotting entry points for pl.umap, pl.tsne, and pl.draw_graph, then inspect how colors are currently selected and how obsm columns are represented. Done means these plots can accept specific principal or diffusion component columns from obsm as color values, with the expected plotting behavior verified by the relevant tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100