Hi,

I would like to use the Leiden algorithm on my scRNAseq to identify the clusters but I cannot run the algorithm. If I use the default one I have no problem. I tried :

 FindClusters(immune.combined, resolution = 0.3, algorithm = 4)

but it gives me this error:

Error: Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg).


In addition: Warning message:
In system2(command = python, args = shQuote(script), stdout = TRUE,  :
  running command ''/Users/camilla/.virtualenvs/r-reticulate/bin/python' '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config/config.py' 2>/dev/null' had status 1

I have reticulate package but when I try to install leidenAlg it install it in a folder I have never seen

The downloaded binary packages are in
    /var/folders/w2/826prqh14cq_pjljhh87q2lh0000gq/T//RtmpkPBi5K/downloaded_packages

and when I try to load it :

library(reticulate)
library('leidenAlg')
library(Matrix)

it gives me this error:

Loading required package: Matrix
Error in value[[3L]](cond) : 
  Package ‘Matrix’ version 1.5.4.1 cannot be unloaded:
 Error in unloadNamespace(package) : namespace ‘Matrix’ is imported by ‘SummarizedExperiment’, ‘SeuratObject’, ‘uwot’, ‘S4Arrays’, ‘spatstat.data’, ‘survival’, ‘spatstat.explore’, ‘DelayedArray’, ‘leiden’, ‘TFisher’, ‘irlba’, ‘reticulate’, ‘spatstat.sparse’, ‘sctransform’, ‘Seurat’ so cannot be unloaded

Why it gives me so many errors? How can I solve it? How can I install pip install leidenalg on R studio?

Thank you

Camilla