UMAP transform
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- Dominant language
- Python
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Description
- [ x] 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?
Is there an option to use umap transform (https://umap-learn.readthedocs.io/en/latest/transform.html) with scanpy? E.g. for embedding new data into the same UMAP space.
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 with the UMAP-learn transform documentation linked in the issue and inspect Scanpy's sc.tools and sc.pl interfaces. The requested result is an option to embed new data into an existing UMAP space; the issue names no specific files or tests, so locating the relevant embedding entry point and validation coverage comes first.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100