UMAP with R

[arararararararar8]

Hello,

I am trying to use umap through R for seurat. What exactly is the code that I should be entering in conda and in R for me to be able to use umap through R?

[lmcinnes]

I am not really an R user, so I don't actually know what to do to get this python version of umap working in R. I believe Seurat has some functionality in this respect, and if you want to use that then you should simply install this package as per the installation instructions. Alternatively there are UMAP packages specifically for R such as UWOT that you can install from CRAN.

[peekxc]

Stumbled upon this issue. It should be quite straightforward to use UMAP w/ reticulate, unless you really want to another package...

E.g.

umap <- import("umap") ## installed from pip via umap-learn module
reducer <- umap$UMAP(n_components=2L, n_neighbors=15L)
umap_emb <- reducer$fit_transform(dataset)

[lmcinnes]

Good to know, thanks. I'm not an R user so a lot of this is a mystery to me.