Change cell size for cust tSNEs from 5 to 2.5

r.scripts/sc-TissueMapper.R

@@ -856,15 +856,15 @@ sctSNECustCol <- function(sc10x,i,bl,rd){
   sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd))
   postscript(paste0("./analysis/diy/tSNE_",i,".CustCol.eps"))
   if (length(bl)==1 & length(rd)==1){
-    plot <- TSNEPlot(object=sc10x,pt.size=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 <- 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)
   } else {
     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)]))
+      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((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 <- TSNEPlot(object=sc10x,pt.size=2.5,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)))
@@ -876,7 +876,7 @@ sctSNECustCol <- function(sc10x,i,bl,rd){
 sctSNEbwCol <- function(sc10x,i,file){
   sc10x <- SetAllIdent(object=sc10x,id=i)
   postscript(paste0("./analysis/diy/tSNE_",file,"_",i,".bwCol.eps"))
-  plot <- TSNEPlot(object=sc10x,pt.size=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 <- 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))
   plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
   plot(plot)