scverse / scverse/scanpy

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.

  1. The documentation of sc.tl.tsne and sc.external.tl.phate weren't updated to indicate that X_{tsne,phate} are obs*m* fields
  2. The documentation of both sc.tl.tsne and sc.tl.umap don't indicate the addition of the uns dictionary with the details of the embedding parameters
  3. The uns dictionaries returned by sc.tl.tsne and sc.tl.umap don't seem to follow the same logic: tsne's param dictionary holds most of the adjustable parameters (even irrelevant ones like n_jobs), while the umap dictionary holds only a and b parameters.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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