I am trying to cluster my single cell data using known markers with the aim of finding cell populations based on expression of specific markers. I am analyzing my data using the Seurat package and ran the following lines of code to get my desired output.
ctrl_BL <- RunPCA(ctrl_BL, approx=FALSE, verbose = FALSE) ctrl_BL <- RunUMAP(ctrl_BL, dims=NULL, features=c("CCL3","CCL5"),verbose = FALSE) ctrl_BL <- FindNeighbors(ctrl_BL, dims=NULL, features=c("CCL3","CCL5"), verbose = FALSE) ctrl_BL <- FindClusters(ctrl_BL, verbose = FALSE) DimPlot(ctrl_BL, label = TRUE) + NoLegend()
However, the resulting plot looks a bit weird to me (see attached). Could you advise me if this is expected or if I am doing anything wrong. I am new to this type of analysis so suggestions are welcome.