Hi All,
I am analysing Single-cell RNAseq data with Seurat. When I cluster my samples using "FindClusters", Seurat starts cluster labels from 0 (Zero) instead of 1. is there a way where I can ask Seurat to start cluster numbers from 1 instead of 0?
Thanks a lot for your help! Have a great day ahead.
Dave.
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David_emir
The newer versions of Seurat start with 1 instead of 0. However, since the clusters are stored as a column in a data.frame, it's easy to change them as necessary.
seurat_object$seurat_clusters <- as.factor(as.numeric(as.character(seurat_object$seurat_clusters)) + 1)
Thanks a lot for your kind help, but when I run this code, my seurat clusters are starting from 2 instead of 1. please have a look
> alldata$seurat_clusters <- as.factor(as.numeric(alldata$seurat_clusters) + 1)
> cbind(table(alldata$seurat_clusters))
[,1]
2 2334
3 2086
4 2077
5 1961
I updated the code so it should work now. This was caused by as.numeric returning the factor levels instead of the the values.
Thanks a lot for your help, i am now able to get seurat clusters from 0 , but when i plot the UMAP or TSNE or PCA all labels still show from '0'th cluster.
DimPlot(alldata, reduction = "UMAP_on_CCA", label=T)
Try specifying which metadata column to use explicitly.
You can either set the identities.
Idents(alldata) <- "seurat_clusters"
Or you can specify what to use in the plotting function.
DimPlot(alldata, reduction = "UMAP_on_CCA", label=T, group.by="seurat_clusters")
Thanks a lot, this really works like a charm. Have a great day ahead.
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I've subsetted out a couple of clusters from a project of mine, but I'm trying to plug the numeric hole in my data. Is there a way to change the numbering of a Seurat cluster from, say, 10 to 9? Thanks!