Chapter 10 Add Custom Annotation

library(Seurat)
library(tidyverse)
library(magrittr)

10.1 Load seurat object

combined <- readRDS('data/Demo_CombinedSeurat_SCT_Preprocess_FilterLQCells.rds')

10.2 Add custom annoation

Method 1 when update annotaiton for all cells

Idents(combined) <- 'SCT_snn_res.0.5'
DimPlot(combined, label = T)

new.cl <- c('InMGE', 'ExN', 'ExM', 'InCGE', 'ExU', 'ExU', 'ExM', 'RG', 'ExDp', 'IP', 
            'InCGE', 'Cycling', 'InMGE', 'OPC', 'End', 'InPSB', 'Mic', 'Per')
names(new.cl) <- levels(combined)
combined <- RenameIdents(combined, new.cl)

DimPlot(combined, label = T)

Method 2 when update annotation for subset cells or try to modify annotation

RG = c(7)
OPC = c(16)
Cycling = c(13)
IP = c(9)

ExN = c(1)
ExM = c(2,6)
ExU = c(5,4)
ExDp = c(8)

InMGE = c(0,14)
InCGE = c(3,11)
InPSB = c(18)

Mic = c(20)
Per = c(21)
End = c(17)


cl.mat <- cbind(c(rep("RG", length(RG)), rep("OPC", length(OPC)), rep("Cycling", length(Cycling)), rep("IP", length(IP)),
                  rep("ExN", length(ExN)), rep("ExM", length(ExM)), rep("ExU", length(ExU)),  rep("ExDp", length(ExDp)),
                  rep("InMGE", length(InMGE)),  rep("InCGE", length(InCGE)),  rep("InPSB", length(InPSB)), 
                   rep("Mic", length(Mic)),  rep("Per", length(Per)),  rep("End", length(End))
                  ),
                c(RG, OPC, Cycling, IP, ExN, ExM, ExU, ExDp, InMGE, InCGE, InPSB, Mic, Per, End))

cl.vec <- combined$SCT_snn_res.0.5
ct.vec <- rep(NA, length(cl.vec))
for(x in unique(cl.mat[,1])){
  cl.x <- cl.mat[cl.mat[,1]==x,2]
  ct.vec[which(cl.vec%in%cl.x)] <- x
}
combined$cluster <- ct.vec

combined$cluster <- factor(combined$cluster, levels = c('RG', 'Cycling','OPC', 'IP', 
                                                        'ExN', 'ExM', 'ExU', 'ExDp', 
                                                        'InMGE', 'InCGE', 'InPSB', 
                                                        'Mic', 'Per', 'End'))
DimPlot(combined, group.by = 'cluster', label = T)

saveRDS(combined, file = 'data/Demo_CombinedSeurat_SCT_Preprocess_FilterLQCells.rds')