Update D17 Cust figs

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -184,9 +184,9 @@ if (any(levels(sc10x@ident)=="Unknown")){
 #pc.use.epi <- results[[3]]
 #rm(results)
 
-sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
+#sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
 #sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.2,folder="epi")
-sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
+#sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
 sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
 
 gene.set1 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
@@ -236,9 +236,9 @@ rm(OE.cells)
 #pc.use.st <- results[[3]]
 #rm(results)
 
-sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.1,folder="st")
+#sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.1,folder="st")
 #sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.2,folder="st")
-sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.5,folder="st")
+#sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.5,folder="st")
 sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=opt$res.st,folder="st")
 
 gene.set1 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
@@ -358,10 +358,10 @@ for (i in ls(pattern="^genes.deg")){
   write.table(get(i),file=paste0("./analysis/deg/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 }
 
-sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St")
-sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"))
-sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="")
-sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"))
+sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D17")
+sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"),file="D17")
+sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="",file="D17")
+sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"),file="D17")
 
 sctSNEbwCol(sc10x,i="res0.2",file="ALL")
 sctSNEbwCol(sc10x.Epi,i="res0.2",file="Epi")
@@ -371,19 +371,19 @@ sctSNEbwCol(sc10x.Epi,i="Epi.dws.sub",file="Epi")
 sctSNEbwCol(sc10x.St,i="St.go",file="St")
 
 for (g in c("Epi","St")){
-  sctSNEHighlight(sc10x,i="Lin",g=g)
+  sctSNEHighlight(sc10x,i="Lin",g=g,file="D17")
 }
 for (g in c("BE","LE","OE1","OE2")){
-  sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g)
-  sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g)
+  sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D17")
+  sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g,file="D17")
 }
-sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE")
+sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE",file="D17")
 for (g in c("Fib","SM","Endo","Leu")){
-  sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g)
-  sctSNEHighlight(sc10x.St,i="St.go",g=g)
+  sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D17")
+  sctSNEHighlight(sc10x.St,i="St.go",g=g,file="D17")
 }
 for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via")){
-  sctSNEHighlight(sc10x,i="samples",g=g)
+  sctSNEHighlight(sc10x,i="samples",g=g,file="D17")
 }
 rm(g)