Exporting Seurat Object Data by Cluster - r

Question

I'm using Seurat to perform a single cell analysis and am interested in exporting the data for all cells within each of my clusters. I tried to use the below code but have had no success.
My Seurat object is called Patients. I also attached a screenshot of my Seurat object. I am looking to extract all the clusters (i.e. Ductal1, Macrophage1, Macrophage2, etc...)
meta.data.cluster <- unique(x = Patients#meta.data$active.ident)
for(group in meta.data.cluster) {
group.cells <- WhichCells(object = Patients, subset.name = "active.ident" , accept.value = group)
data_to_write_out <- as.data.frame(x = as.matrix(x = Patients#raw.data[, group.cells]))
write.csv(x = data_to_write_out, row.names = TRUE, file = paste0(save_dir,"/",group, "_cluster_outfile.csv"))
}
I am new to R and coding so any help is greatly appreciated! :)

Answer 1

It doesn't work because there is no active.ident column under your metadata. For example if we use an example dataset like yours and set the ident:
library(Seurat)
M = matrix(rnbinom(5000,mu=20,size=1),ncol=50)
colnames(M) = paste0("P",1:50)
rownames(M) = paste0("gene",1:100)
Patients = CreateSeuratObject(M)
Patients$grp = sample(c("Ductal1","Macrophage1","Macrophage2"),50,replace=TRUE)
Idents(Patients) = Patients$grp
You can see this line of code gives you no value:
meta.data.cluster <- unique(x = Patients#meta.data$active.ident)
meta.data.cluster
NULL
You can do:
meta.data.cluster <- unique(Idents(Patients))
for(group in meta.data.cluster) {
group.cells <- WhichCells(object = Patients, idents = group)
data_to_write_out <- as.data.frame(GetAssayData(Patients,slot = 'counts')[,group.cells])
write.csv(data_to_write_out, row.names = TRUE, file = paste0(save_dir,"/",group, "_cluster_outfile.csv"))
}
Note also you can get the counts out using GetAssayData . You can subset one group and write out like this:
wh <- which(Idents(Patients) =="Macrophage1" )
da = as.data.frame(GetAssayData(Patients,slot = 'counts')[,wh])
write.csv(da,...)