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I was trying to analysis a set of singe cells RNAseq data by Seurat in R. I made the UMAP by running

SCIs <- RunUMAP(SCIs, dims = 1:20)
P1 <- DimPlot(SCIs, reduction = "umap", raster = FALSE)
P1

It gives UMAP with cluster label (1 to 12), however I also want the plot labeled by Stages in SCIs@meta.data$Stage, in total it has three stages labeled each cell. So I add

LabelClusters(plot = P1,id = SCIs@meta.data$Stage)

however, I got this error

Error: C stack usage  7969206 is too close to the limit
In addition: Warning message:
In if (!id %in% colnames(x = plot$data)) { :
  the condition has length > 1 and only the first element will be used

I saw some sources say it's not because of memory but due to recursion. I'm confused. Please help.

Thanks

neilfws
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  • It's easier to help you if you include a simple [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input and desired output that can be used to test and verify possible solutions. – MrFlick Feb 27 '23 at 21:39

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