0
$\begingroup$

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?

M@active.ident <- M@meta.data$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(M@meta.data) 
        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..

$\endgroup$
1
$\begingroup$

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

or more explicitly

M <- SetIdent(M, value = M@meta.data$status)

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

| improve this answer | |
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.