Comments (2)
Thanks a lot.
But still for whatever reason, I am still not capable of getting the color code associated with the cells. But I guess this is question for the Seurat team.
Appreciate your help, and thanks for this tool.
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Hi, thanks for your inquiry. I'm not super familiar with Seurat, but it looks like you can get cell embeddings via Embeddings
function.
Based on this tutorial, you can do something like:
library(Seurat)
pbmc <- readRDS(file = "../data/pbmc3k_final.rds")
input <- Embeddings(pbmc, reduction = "umap")[, 1:6]
To get the first six components of the UMAP embeddings and use it as an input to grimon. Please also have a look at our documentation about the input format.
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