How to generate Cluster annotation file about scapa HOT 1 OPEN

If you have already added cell type annotation as in metadata column of your Seurat object, you can use the following code:

Extract cell type annotation
meta_dat<-as.data.frame([email protected]$cell_type)

Add barcodes as 1st column to this table
meta_dat<-cbind(rownames([email protected]),meta_dat)
rownames(meta_dat)<-NULL

Save table in current directory (or change the code to add it to desired output directory)

write.table(x = meta_dat,
file = 'project1_cell_type_annotation.txt'),
sep = '\t', row.names = F, col.names = F, quote = F)

from scapa.