Commit 484ea5ec authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Fix endo labeling from singler

parent 1337e208
......@@ -20,11 +20,12 @@ cells.club <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1
cells.ne <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="NE",])
cells.fib <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="Fib",])
cells.sm <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="SM",])
cells.endo <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="Endo",])
cells.epi <- c(cells.be,cells.le,cells.hillock,cells.club,cells.ne)
cells.fmst <- c(cells.fib,cells.sm)
cells.st <- c(cells.fmst,cells.endo)
cells.leu <- cells.leu <-names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="Leu",])
cells.leu <- names(singler$singler[[1]]$SingleR.single$labels[singler$singler[[1]]$SingleR.single$labels[,1]=="Leu",])
Idents(sc10x,cells=cells.epi) <- "Epi"
Idents(sc10x,cells=cells.fmst) <- "FMSt"
......
......@@ -29,8 +29,7 @@ scFolders()
sc10x <- scLoad(p=project.name,cellranger=3,ref="GRCh38")
lu=0
results <- scQC(sc10x,lu=lu,sub=FALSE,sp="hu")
results <- scQC(sc10x,sub=FALSE,sp="hu")
sc10x <- results[[1]]
counts.cell.raw <- results[[2]]
counts.gene.raw <- results[[3]]
......
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