SingleR Cluster-wise annotation

Hi,
I have been trying to use SingleR to annotate the cell type per cluster.
I used my Seurat object from integration analysis and the code was:

ref <- ImmGenData()
pred <- SingleR(as.SingleCellExperiment(seurat.integrated), ref, labels=ref$label.main, clusters=Idents(seurat.integrated))

But, when I checked rownames(pred), it still showed the name of each cell, not the cluster ids that I input in the function.
Also, when I checked with table(pred$labels), it also showed the number of a single cell per cell type.

Could anyone help me get the cluster-wise annotation results (the code above only provided me a single-cell wise annotation results)?

Any advice will be greatly appreciated. Thank you!


Seurat


SingleR


annotation


scRNA-seq


CellType

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