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Documentation inconsistencies and mistakes - tools / embeddings / tsne, phate, umap #2408

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yotamcons opened this issue Feb 8, 2023 · 1 comment
Open
3 tasks done

Documentation inconsistencies and mistakes - tools / embeddings / tsne, phate, umap #2408

yotamcons opened this issue Feb 8, 2023 · 1 comment

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@yotamcons
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yotamcons commented Feb 8, 2023 •
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  • 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.
@Zethson
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Zethson commented Feb 15, 2023

We'd appreciate PRs that fix these! Thanks.

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@Zethson @yotamcons