Fixed folder references for QuSAGE Epi + LGES.St & changed output folder for Tables

r.scripts/sc_QuSAGE.Epi.R

@@ -255,7 +255,7 @@ rm(BE)
 rm(LE)
 rm(OE)
 rm(merge.cluster)
-png(paste0("./anaysis/",opt$g,"/global",sub.folder,"/tSNE_EpiSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_EpiSubPop.png"),1000,1000,pointsize=20)
 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)))

r.scripts/sc_QuSAGE.LGEA.St.R

@@ -209,7 +209,7 @@ rm(MylImm.cells)
 rm(UK.cells)
 
 #generate LGEA StPops tSNE
-png(paste0("./"analysis/,opt$g,"/global",sub.folder,"/tSNE_LGEA.St.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_LGEA.St.png"),1000,1000,pointsize=20)
 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)))

r.scripts/sc_Tables.R

@@ -31,10 +31,13 @@ rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst")
 if (!dir.exists(paste0("./analysis/",opt$g))){
   dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./analysis/",opt$g,"/table"))){
-  dir.create(paste0("./analysis/",opt$g,"/table"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
+}
+if (!dir.exists(paste0("./analysis/",opt$g,"/global/table"))){
+  dir.create(paste0("./analysis/",opt$g,"/global/table"))
 }
 
-write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./analysis/",opt$g,"/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./analysis/",opt$g,"/global/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")