Commit 5718fa8f authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Add NE feature plots to diy

parent 08ca3d3e
......@@ -211,3 +211,7 @@ for (i in c("BE","LE","Hillock","Club","NE","Fib","SM")){
deg <- FindAllMarkers(data,assay="SCT",slot="data",logfc.threshold=0,test.use="MAST")
write.table(deg,file=paste0("./analysis/vis/diy/DEG_pheno.",i,".csv"),sep=",",quote=FALSE,row.names=FALSE,col.names=TRUE)
}
postscript(paste0("./analysis/vis/diy/UMAP_epi.CHGA.eps"))
FeaturePlot(sc10x.epi,features="CHGA",cols=c("lightgrey","darkred"),pt.size=2.5)+theme_cowplot()
dev.off()
......@@ -252,3 +252,7 @@ sc10x.epi <- RenameIdents(sc10x.epi,"APr LE"="APrLE")
sc10x.epi$CellType <- Idents(sc10x.epi)
sc10x.epi$CellType <- factor(sc10x.epi$CellType,levels=c("BE","Ur","VPrLE","DLPrLE","APrLE","ED"))
results <- scQuSAGE(sc10x.epi,gs=E.MTAB.4991,type="sm",id="CellType",nm="E.MTAB.4991",print="umap")
postscript(paste0("./analysis/vis/diy/UMAP_epi.Calca.eps"))
FeaturePlot(sc10x.epi,features="Calca",cols=c("lightgrey","darkred"),pt.size=2.5)+theme_cowplot()
dev.off()
\ No newline at end of file
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