Fix QuSAGE save ID for large datasets

r.scripts/sc-TissueMapper_functions.R

@@ -361,7 +361,7 @@ scCluster <- function(sc10x,res=0.1,red="pca",dim,print="tsne",folder=FALSE){
   plot2 <- DimPlot(sc10x,reduction="tsne",group.by="samples")
   plot3 <- DimPlot(sc10x,reduction="umap",group.by="samples")
   legend <- cowplot::get_legend(plot1)
-
+  
   if (print=="tsne"){
     postscript(paste0("./analysis/vis/",sub,"tSNE_samples.eps"))
     grid.arrange(plot2,legend,ncol=1)
@@ -579,23 +579,21 @@ scQuSAGE <- function(sc10x,gs,save=FALSE,type,id,ds=0,nm="pops",print="tsne"){
     if (max(qs$path.PDF)>max.y.rg){
       max.y.rg <- max(qs$path.PDF)
     }}
-  
-  #Plot correlation plots by geneset
-  for (i in 1:length(gs)){
-    postscript(paste0("./analysis/cor/",nm,"/geneset/QuSAGE_",nm,".",names(gs)[i],".eps"))
-    for (j in groups){
-      qs <- get(paste0("results.",j))
-      if (j==groups[1]){
-        plotDensityCurves(qs,path.index=i,col=col[match(j,groups)],main=names(gs)[i],xlim=c(min.x.rg-0.05,max.x.rg+0.05),ylim=c(0,50*ceiling(max.y.rg/50)),xlab="Gene Set Activation",lwd=5,cex.main=2.5,cex.axis=1.5,cex.lab=2)
-      } else {
-        plotDensityCurves(qs,path.index=i,add=TRUE,col=col[match(j,groups)],lwd=5)
-      }}
-    legend("topright",col=col,legend=groups,lty=1,lwd=5,cex=2,ncol=1,bty="n",pt.cex=2)
-    box(lwd=5)
-    dev.off()
-  }
-  
   if (type=="sm"){
+    #Plot correlation plots by geneset
+    for (i in 1:length(gs)){
+      postscript(paste0("./analysis/cor/",nm,"/geneset/QuSAGE_",nm,".",names(gs)[i],".eps"))
+      for (j in groups){
+        qs <- get(paste0("results.",j))
+        if (j==groups[1]){
+          plotDensityCurves(qs,path.index=i,col=col[match(j,groups)],main=names(gs)[i],xlim=c(min.x.rg-0.05,max.x.rg+0.05),ylim=c(0,50*ceiling(max.y.rg/50)),xlab="Gene Set Activation",lwd=5,cex.main=2.5,cex.axis=1.5,cex.lab=2)
+        } else {
+          plotDensityCurves(qs,path.index=i,add=TRUE,col=col[match(j,groups)],lwd=5)
+        }}
+      legend("topright",col=col,legend=groups,lty=1,lwd=5,cex=2,ncol=1,bty="n",pt.cex=2)
+      box(lwd=5)
+      dev.off()
+    }
     #Plot correlation plots by cluster
     for (i in groups){
       qs <- get(paste0("results.",i))
@@ -621,7 +619,7 @@ scQuSAGE <- function(sc10x,gs,save=FALSE,type,id,ds=0,nm="pops",print="tsne"){
     merge.cluster <- NULL
     for (i in groups){
       if (max(qsTable(get(paste0("results.",i)),number=length(gs))[qsTable(get(paste0("results.",i)),number=length(gs))[,4]<=0.05,][,2],na.rm=TRUE)>=0){
-        sc10x<-eval(parse(text=paste0("RenameIdents(object=sc10x,'",sub("Cluster_","",i),"' = '",qsTable(get(paste0("results.",i)),number=length(gs))[qsTable(get(paste0("results.",i)),number=length(gs))[2]==max(qsTable(get(paste0("results.",i)),number=length(gs))[qsTable(get(paste0("results.",i)),number=length(gs))[,4]<=0.05,][,2])][1],"')")))
+        sc10x<-eval(parse(text=paste0("RenameIdents(object=sc10x,'",sub("Cluster_","",i),"' = '",qsTable(get(paste0("results.",i)),number=length(gs))[qsTable(get(paste0("results.",i)),number=length(gs))[2]==max(qsTable(get(paste0("results.",i)),number=length(gs))[qsTable(get(paste0("results.",i)),number=length(gs))[,4]<=0.05,][,2],na.rm=TRUE)][1],"')")))
       } else {
         sc10x<-eval(parse(text=paste0("RenameIdents(object=sc10x,'",sub("Cluster_","",i),"' = 'Unknown')")))
       }}