I was supposed to use the code below to get the number of cells per cluster. The code works with Seurat version 2, but while using version 3 I got the error no slot of name "ident" for this object of class "Seurat"
. Does anyone have any idea about how to deal with this?
# Calculate number of cells per cluster from object@ident
cell.num <- table(shox2crepos_mtmg@ident)
# Add cell number per cluster to cluster labels
ClusterLabels = paste("Cluster", names(cell.num), paste0("(n = ", cell.num, ")"))
# Order legend labels in plot in the same order as 'ClusterLabels'
ClusterBreaks = names(cell.num)
# Plot tSNE with new legend labels for clusters
TSNEPlot(object = shox2crepos_mtmg, do.return = T) +
scale_colour_discrete(breaks = ClusterBreaks,
labels = ClusterLabels) +
labs(x = "t-SNE 1",
y = "t-SNE 2")
cheat sheet
page with all the different commands betweenv2
andv3
(Seurat v2.X vs v3.X
). $\endgroup$