Make Lin identity with St+Unknown merge and diy figs

r.scripts/sc-TissueMapper_RUN.Pd.R

@@ -331,6 +331,10 @@ sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws_St.go",i.2="NE",nm=
 
 sc10x.Epi <- scMerge(sc10x.Epi,sc10x.Epi,sc10x.Epi.NE,i.1="Epi.dws.sub",i.2="NE",nm="Epi.dws.sub_NE")
 
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
+sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[sc10x@ident %in% c("St","Unknown")]),ident.use="St")
+sc10x <- StashIdent(object=sc10x,save.name="mLin")
+
 gene.orthog <- read.delim("./genesets/Ensemble.mus-hum.txt")
 gene.set1 <- read_csv("./genesets/SupTab3_Consensus_Sigs.csv",skip=6)
 gene.set2 <- as.data.frame(gene.set1$Basal[!is.na(gene.set1$Basal)])
@@ -478,6 +482,7 @@ for (i in ls(pattern="^genes.deg")){
 }
 
 sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D")
+sctSNECustCol(sc10x,i="mLin",bl="Epi",rd="St",file="D")
 sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"),file="D")
 sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="",file="D")
 sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"),file="D")
@@ -492,6 +497,7 @@ sctSNEbwCol(sc10x.St,i="St.go",file="St",files="D")
 for (g in c("Epi","St","Unknown")){
   sctSNEHighlight(sc10x,i="Lin",g=g,file="D")
 }
+sctSNEHighlight(sc10x,i="mLin",g=c("St"),file="D")
 for (g in c("BE","LE","OE1","OE2")){
   sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D")
   sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g,file="D")