scanpy.tl.umap should have a `key_added` parameter
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- Dominant language
- Python
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Description
If you have multiple neighbors graphs, you can only store the computed UMAP coordinates of one of them in an anndata with sc.tl.umap. Instead, it should be possible to store multiple UMAP embeddings computed from multiple sc.tl.umap(neighbors_key=X).
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 at the sc.tl.umap entry point and inspect how coordinates are stored when neighbors_key is selected. Add support for a key_added destination so UMAP embeddings from multiple neighbors graphs can coexist, and verify that each embedding is stored under its requested key.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100