Embedding density limited to 10 groups?
See original GitHub issue@LuckyMD, why does sc.tl.embedding_density
limit itself to running on labels with 10 or less categories?
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- State:
- Created 4 years ago
- Comments:6 (6 by maintainers)
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Embedding density limited to 10 groups? · Issue #719 - GitHub
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I think it can help for when groups overlap. When two solid colors overlap, you lose visual information. Here you may be able to plot multiple groupings on the same plot, since there are no fills so it’s more likely you can disambiguate the boundaries when overlaps occur.
Having run into the limitations of constraining to 10 categories for quite some time, and now seeing @sunnysun515 write a wrapper that brings the functionality and produces meaningful plots: I’d strongly advocate for letting the user decide!
To address concerns raised above, I added a warning to the docstring that enough cells per category are needed for a meaningful estimate: https://github.com/theislab/scanpy/pull/1936/commits/760a967b57b93b0da3296d98430509627f3a80d7
[Imagining a warning showing up whenever the function is called seems more disruptive.]
Otherwise, it’d be great if @LuckyMD and @sunnysun515 could take a look in addition to Isaac: https://github.com/theislab/scanpy/pull/1936