How to use Leiden clustering with Seurat?

[lm687]

Using reticulate - Carla, can we get the solution here? We had a minimal example. thanks

[liezeltamon]

This is what I do and it works also even when using renv:

Preparing conda environment with leidenalg for Seurat::FindClusters() (Last update: 2024-05-31)

• reticulate R package will be used to load leidenalg python module and dependencies numpy and pandas

mamba create -n leiden leidenalg numpy pandas

Using leidenalg in R

• Set RETICULATE_PYTHON in .Renviron to path of python environment with the packages for reticulate to find. For example:

RETICULATE_PYTHON=/project/sims-lab/ltamon/mamba_installation/conda/envs/leiden/bin/python

• In R:

library(reticulate)
reticulate::import("numpy")
reticulate::import("pandas")
reticulate::import("leidenalg")

[kevinrue]

Check out basilisk (Bioconductor) https://joss.theoj.org/papers/10.21105/joss.04742

Happy to explain more if needed