Fix QuSAGE x-axis and some diy cust cols

r.scripts/sc-TissueMapper.R

@@ -559,9 +559,10 @@ scQuSAGE <- function(sc10x,gs,res.use=0.1,ds=25000,nm="Lin",folder="lin"){
     qs <- get(paste0("results.",i))
     if (max(qs$path.mean)>max.x.rg){
       max.x.rg <- max(qs$path.mean)
-      if (min(qs$path.mean)<min.x.rg){
-        min.x.rg <- min(qs$path.mean)
-      }}
+    }
+    if (min(qs$path.mean)<min.x.rg){
+      min.x.rg <- min(qs$path.mean)
+    }
     if (max(qs$path.PDF)>max.y.rg){
       max.y.rg <- max(qs$path.PDF)
   }}
@@ -694,9 +695,10 @@ scQuSAGEsm <- function(sc10x,gs,ds=25000,nm="Lin",folder="lin"){
     qs <- get(paste0("results.",i))
     if (max(qs$path.mean)>max.x.rg){
       max.x.rg <- max(qs$path.mean)
-      if (min(qs$path.mean)<min.x.rg){
-        min.x.rg <- min(qs$path.mean)
-      }}
+    }
+    if (min(qs$path.mean)<min.x.rg){
+      min.x.rg <- min(qs$path.mean)
+    }
     if (max(qs$path.PDF)>max.y.rg){
       max.y.rg <- max(qs$path.PDF)
     }}
@@ -1153,10 +1155,14 @@ sc3CCA <-  function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=
 
 sctSNECustCol <- function(sc10x,i,bl,rd,file){
   sc10x <- SetAllIdent(object=sc10x,id=i)
-  sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd))
+  sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd,"Unknown"))
   postscript(paste0("./analysis/diy/tSNE_",file,".",i,".CustCol.eps"))
   if (length(bl)==1 & length(rd)==1){
-    plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5]))
+    if (length(sc10x@ident[sc10x@ident=="Unknown"])>0){
+      plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5],"grey50"))
+    } else {
+      plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5]))
+    }
     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)
@@ -1175,6 +1181,7 @@ sctSNECustCol <- function(sc10x,i,bl,rd,file){
 
 sctSNEbwCol <- function(sc10x,i,file,files){
   sc10x <- SetAllIdent(object=sc10x,id=i)
+  sc10x@ident <- factor(sc10x@ident,levels=c("Epi","BE","LE","OE1","OE_SCGB","OE2","OE_KRT13","St","Fib","SM","Endo","Leu","Unknown",1:10))
   postscript(paste0("./analysis/diy/tSNE_",files,".",file,"_",i,".bwCol.eps"))
   plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=colorRampPalette(c("white","black"))(length(unique(sc10x@ident))+2)[3:(length(unique(sc10x@ident))+2)])
   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))

r.scripts/sc-TissueMapper_RUN.Pd.R

@@ -489,7 +489,7 @@ sctSNEbwCol(sc10x,i="Merge_Epi.dws_St.go",file="ALL",files="D")
 sctSNEbwCol(sc10x.Epi,i="Epi.dws.sub",file="Epi",files="D")
 sctSNEbwCol(sc10x.St,i="St.go",file="St",files="D")
 
-for (g in c("Epi","St")){
+for (g in c("Epi","St","Unknown")){
   sctSNEHighlight(sc10x,i="Lin",g=g,file="D")
 }
 for (g in c("BE","LE","OE1","OE2")){