Commit d0b0d4e5 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Calculate DEGs with hu Urethra merged

parent ce20676a
......@@ -149,6 +149,15 @@ dev.off()
postscript(paste0("./analysis/vis/diy/UMAP_epi.pops.split.eps"))
DimPlot(sc10x.epi,split.by="Phenotype")+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
Idents(sc10x.epi) <- "Phenotype"
sc10x.epi.normalpz <- subset(sc10x.epi,idents="Normal Pz")
sc10x.epi.bph <- subset(sc10x.epi,idents="BPH")
postscript(paste0("./analysis/vis/diy/UMAP_epi.pops.split_NormalPz.eps"))
DimPlot(sc10x.epi.normalpz,group.by="Cell.Type")+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
postscript(paste0("./analysis/vis/diy/UMAP_epi.pops.split_BPH.eps"))
DimPlot(sc10x.epi.bph,group.by="Cell.Type")+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
postscript(paste0("./analysis/vis/diy/Dot_epi.pops.anchor.eps"))
DotPlot(sc10x.epi,features=rev(c("KRT5","KLK3","KRT13","SCGB3A1","CHGA")),dot.scale=10,cols=rev(heat.colors(2)))
......@@ -204,6 +213,14 @@ dev.off()
write.table(table(sc10x$`Cell.Type`,sc10x$samples),file="./analysis/vis/diy/Table_pops.Samples.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
write.table(table(sc10x$`Cell.Type`,sc10x$Phenotype),file="./analysis/vis/diy/Table_pops.Phenotype.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
Idents(sc10x) <- "lin"
data <- subset(sc10x,idents="Epi")
Idents(data) <- "Cell.Type"
data <- RenameIdents(data,"Hillock"="Urethra")
data <- RenameIdents(data,"Club"="Urethra")
deg <- FindAllMarkers(data,assay="SCT",slot="data",logfc.threshold=0,test.use="MAST",only.pos=TRUE)
write.table(deg,file=paste0("./analysis/vis/diy/DEG_pheno.Urethra.csv"),sep=",",quote=FALSE,row.names=FALSE,col.names=TRUE)
Idents(sc10x) <- "Cell.Type"
for (i in c("BE","LE","Hillock","Club","NE","Fib","SM")){
data <- subset(sc10x,idents=i)
......
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