UMAP implementation in igraph

[iosonofabio]

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

dear devs,

Thank you for maintaining scanpy, which is a great piece of software.

I am a core developer of igraph and around a year ago we started providing an implementation of UMAP. It is accessible via the igraph Python package and the actual computations run entirely in C. This is designed to be an alternative to the original UMAP implementation that requires numba, llvmlite, etc. Since scanpy relies on igraph for clustering already, this might be useful for folks who have trouble with the dependency stack.

Just like Leiden clustering can now use either leidenalg or directly igraph, it would be nice to let people choose flavor='igraph' for embedding as well.

Our implementation requires as input a nearest neighbor graph with distances and has two parts, just like the original umap:

1. a function to compute what are now called in scanpy "connectivities" from the distances. This is among other things a symmetrysation of the knn graph.
2. a function to compute the embedding from the connectivity graph.

Would you be interested in this? If so, I can make a PR for scanpy and perhaps one of you can review it?

[ricor07]

Hello, I'd be glad to provide this enhancement and joining the project. Can you assign this issue to me? Thanks