LineageSubClust res tSNEs put in global directory when NoStress analysis selected

r.scripts/sc_LineageSubClust.R

@@ -75,7 +75,7 @@ dev.off()
 
 #re-generate tSNE dimensions and generage sample figures
 sc10x.Group.Epi <- RunTSNE(object=sc10x.Group.Epi,dims.use=1:PC.Max,do.fast=TRUE)
-postscript(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Sample.Epi.eps"))
+postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Sample.Epi.eps"))
 plot <- TSNEPlot(object=sc10x.Group.Epi,group.by="samples",pt.size=2.5,do.return=TRUE)
 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)))
@@ -83,7 +83,7 @@ plot(plot)
 dev.off()
 
 sc10x.Group.St <- RunTSNE(object=sc10x.Group.St,dims.use=1:PC.Max,do.fast=TRUE)
-postscript(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Sample.St.eps"))
+postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Sample.St.eps"))
 plot <- TSNEPlot(object=sc10x.Group.St,group.by="samples",pt.size=2.5,do.return=TRUE)
 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)))
@@ -103,7 +103,7 @@ for (j in pops){
     sc10x.Group <- FindClusters(object=sc10x.Group,reduction.type="pca",dims.use=1:PC.Max,resolution=i,print.output=0,save.SNN=TRUE,force.recalc=TRUE)
     sc10x.Group <- BuildClusterTree(sc10x.Group,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
     sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("res",i))
-    postscript(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_SubClust.",j,".res",i,".eps"))
+    postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_SubClust.",j,".res",i,".eps"))
     plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
     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)))