why renaming Idents in Seurat object doesn't work?

[yeroslaviz]

I'm trying to rename my clusters in a Seurat object.

my old cluster IDs are numers

Idents(seuObj) <- 'RNA_snn_res.0.1'
levels(seuObj)
 [1] "0"  "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13" "14" "15"

I would like to assign the clusters names from a named vector

Following the vignette from the web site I tried to assign the vector to the numbers -

cluster_ids <- c("DC2_genes",  "mregDC_genes", "mregDC_genes", "Bcell_genes",...)
names(cluster_ids) <- levels(seuObj)
seuObj <- RenameIdents(seuObj, cluster_ids)

But this just assigns numbers to the new Idents

head(Idents(seuObj))
C7_AAACCCAAGGGTGGGA-1 C7_AAACCCAAGTAGCATA-1 C7_AAACCCACAAGAGGTC-1 C7_AAACCCACAGTCTCTC-1 C7_AAACCCACATGAATCC-1 
    0.346464052287582     0.177389184397163     0.132815134099617     0.300105882352941     0.497196167423096 
C7_AAACCCAGTAGAGGAA-1 
    0.335241176470588 

What am I doing wrong here?

[yeroslaviz]

I manage to find a workwround, but I don't understand what I did wrong here.

my solution was to extract the cluster column as vector and assign the new names to it. Then I created a new column in my seurat obj.

vec <- seuObj $RNA_snn_res.0.1
levels(vec) <- cluster_ids
seuObj[["UCell_clusters"]] <- vec
Idents(seuObj) <- 'UCell_clusters'

[mhkowalski]

Hi,

Glad you were able to find a workaround. I couldn't reproduce this myself, would you be able to provide a reproducible example to get this issue?

Idents(pbmc_small) <- 'RNA_snn_res.0.8'
levels(pbmc_small)
cluster_ids <- c("DC2_genes",  "mregDC_genes")
names(cluster_ids) <- levels(pbmc_small)
pbmc_small <- RenameIdents(pbmc_small, cluster_ids)

head(Idents(pbmc_small))
ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA AGTCAGACTGCACA TCTGATACACGTGT 
     DC2_genes      DC2_genes   mregDC_genes      DC2_genes      DC2_genes      DC2_genes 
Levels: DC2_genes mregDC_genes