Add DIY CustCol and Highlight tSNEs

r.scripts/sc-TissueMapper.R

@@ -849,3 +849,35 @@ scCCA <-  function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
   )
   return(results)
 }
+
+
+sctSNECustCol <- function(sc10x,i,bl,rd){
+  sc10x <- SetAllIdent(object=sc10x,id=i)
+  sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd))
+  postscript(paste0("./analysis/diy/tSNE_",i,".CustCol.eps"))
+  if (bl!=""){
+    plot <- TSNEPlot(object=sc10x,pt.size=5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal((length(bl)+1),"Blues")[2:(length(bl)+1)],brewer.pal((length(rd)+1),"Reds")[2:(length(rd)+1)]))
+  } else {
+    plot <- TSNEPlot(object=sc10x,pt.size=5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=brewer.pal((length(rd)+1),"Reds")[2:(length(rd)+1)])
+
+  }
+  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+  plot(plot)
+  dev.off()
+}
+
+
+sctSNEHighlight <- function(sc10x,i,g){
+  sc10x <- SetAllIdent(object=sc10x,id=i)
+  sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[!(sc10x@ident %in% g)]),ident.use="Background")
+  sc10x@ident <- factor(sc10x@ident,levels=c(g,"Background"))
+  sc10x@data <- sc10x@data[,c(colnames(sc10x@data)[!colnames(sc10x@data) %in% names(sc10x@ident[sc10x@ident==g])],names(sc10x@ident[sc10x@ident==g]))]
+  
+  postscript(paste0("./analysis/diy/tSNE_",i,"_",g,".Highlight.eps"))
+  plot <- TSNEPlot(object=sc10x,pt.size=5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c("darkred","grey"))
+  plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+  plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+  plot(plot)
+  dev.off()
+}

r.scripts/sc-TissueMapper_RUN.D17.R

@@ -6,6 +6,7 @@ library(readr)
 library(fBasics)
 library(pastecs)
 library(qusage)
+library(RColorBrewer)
 
 source("../r.scripts/sc-TissueMapper.R")
 
@@ -74,6 +75,9 @@ if (!dir.exists("./analysis/tSNE/FINAL")){
 if (!dir.exists("./analysis/deg")){
   dir.create("./analysis/deg")
 }
+if (!dir.exists("./analysis/diy")){
+  dir.create("./analysis/diy")
+}
 
 #Retrieve command-line options
 option_list=list(
@@ -352,8 +356,32 @@ 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="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"))
+
+for (g in c("Epi","St")){
+  sctSNEHighlight(sc10x,i="Lin",g=g)
+}
+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.Epi.NE,i="NE",g="NE")
+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)
+}
+for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via")){
+  sctSNEHighlight(sc10x,i="samples",g=g)
+}
+
 save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
 rm(list=ls(pattern="^genes.deg"))
+save(list=ls(pattern="^sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+rm(list=ls(pattern="^sc10x.Epi"))
+save(list=ls(pattern="^sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="^sc10x.St"))
 save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
 rm(list=ls(pattern="^sc10x"))
 save.image(file="./analysis/Data.RData")