Precomputed distance matrices
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- Dominant language
- Python
- Stars
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
I would like to use a precomputed distance or affinity matrix with many of the tools in scanpy. Currently this feature is unsupported. It should be a relatively small PR - essentially adding "precomputed_key" to sc.pp.neighbors etc that specifies a key in obsp to look for distances.
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 reading sc.pp.neighbors and identifying the other Scanpy tools intended to accept a precomputed distance or affinity matrix from obsp. Confirm the affected scope and expected behavior before changing anything; done means those tools can use the requested precomputed_key without requiring a newly computed matrix.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100