Compute UMAP from pre-existing distance matrix
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- Python
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Description
It should be easier to compute a UMAP layout from a pre-existing distance matrix. Currently, we only really support this for pre-existing connectivity matrices.
The missing step here is computing the umap weighted graph from a distance matrix.
The functionality for this largely already exists in the sc.neighbors module in private functions (example: https://github.com/theislab/scanpy/issues/2139#issuecomment-1050914072). We would just need an API.
Previously discussed in: #1561
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 in the private functions in the sc.neighbors module referenced by the issue, then review the discussion in #1561 and the linked comment for existing distance-matrix behavior. Define the public API for producing a UMAP weighted graph from a pre-existing distance matrix and verify that the resulting layout follows the existing connectivity-matrix path.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization, machine-learning
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100