Documentation inconsistencies and mistakes - tools / embeddings / tsne, phate, umap
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Description
- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
- (optional) I have confirmed this bug exists on the master branch of scanpy.
- The documentation of
sc.tl.tsneandsc.external.tl.phateweren't updated to indicate thatX_{tsne,phate}areobs*m*fields - The documentation of both
sc.tl.tsneandsc.tl.umapdon't indicate the addition of theunsdictionary with the details of the embedding parameters - The
unsdictionaries returned bysc.tl.tsneandsc.tl.umapdon't seem to follow the same logic: tsne's param dictionary holds most of the adjustable parameters (even irrelevant ones liken_jobs), while the umap dictionary holds only a and b parameters.
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 documentation and implementations for sc.tl.tsne, sc.external.tl.phate, and sc.tl.umap, then inspect the returned obs and uns entries. Document the embedding fields and parameter dictionaries, and determine a consistent representation for the tsne and umap metadata; done means the documentation and behavior are consistent.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- documentation, machine-learning
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100