Hello everyone, I used SEURAT for scRNA-seq analysis from where I generated different clusters in UMAP plot. Next, I want to do the diffusion mapping to see which cluster have a central core.

The library that I m using is called destiny and the code is this:

dm_guo <- DiffusionMap(guo, verbose = FALSE,
censor_val = 15, censor_range = c(15, 40))

The script requires a matrix or a data.frame but if I extract the matrix from my analysis I will loose the UMAP clusters informations, so I’m looking for a way to link SEURAT result to diffusionMAP code.

Any suggestion will help since I have no idea how to do this

thanks very much