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Changing active.ident in Seurat

Bioinformatics Asked on January 1, 2022

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn’t. I don’t understand how to fix it?

[email protected] <- [email protected]$status
Error in (function (cl, name, valueClass)  : 
assignment of an object of class “character” is not valid for @‘active.ident’ in an object of class 
“Seurat”; is(value, "factor") is not TRUE

head([email protected]) 
        orig.ident nCount_RNA nFeature_RNA percent.mito   status  RNA_snn_res.0.6 seurat_clusters 
BC03_03       BC03   998414.7         3356   0.07869098 nonTumor                0               0
BC03_09       BC03   999853.6         7616   0.12964336  primary                0               0
BC03_13       BC03   998206.5         8457   0.17672205  primary                0               0
BC03_17       BC03   999535.1         7494   0.11323008  primary                0               0

I want to run the UMAP with the clusters named according to the status and not seurat clusters.However, the code isnt working..

One Answer

M <- SetIdent(M, value = "status")

or more explicitly

M <- SetIdent(M, value = [email protected]$status)

You can also use the group.by argument of UMAPPlot() or other plotting functions from Seurat for that matter.

Answered by haci on January 1, 2022

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