question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

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?

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:6 (6 by maintainers)

github_iconTop GitHub Comments

1reaction
ivirshupcommented, Dec 2, 2019

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.

0reactions
falexwolfcommented, Jul 7, 2021

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

Read more comments on GitHub >

github_iconTop Results From Across the Web

Embedding density limited to 10 groups? · Issue #719 - GitHub
I came across this when I wanted to look at the densities of two clusters (out of a clustering solution with ~15) without...
Read more >
scanpy.tl.embedding_density — Scanpy 1.9.1 documentation
The embedding dimensions over which the density should be calculated. This is limited to two components. Return type. None. Returns. Updates adata.obs ...
Read more >
Extending density functional embedding theory for covalently ...
The uniqueness of the local embedding potential in DFET essentially is rooted in the Hohenberg–Kohn theorem (10, 18), which states that there is ......
Read more >
A Simple, Exact Density-Functional-Theory Embedding Scheme
Density functional theory (DFT) provides a formally exact framework for quantum embedding. The appearance of nonadditive kinetic energy ...
Read more >
Density embedding with constrained chemical potential
Our density embedding method can be used to define fragments even at finite separations. We show that using these definitions for fragments, the ......
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found