Make one set of tables with all samples

r.scripts/sc_Tables.R

@@ -63,13 +63,9 @@ sc10x.Group@meta.data$'SubClust.ID+NE' <- factor(sc10x.Group@meta.data$'SubClust
   rev(unique(as.character(sc10x.Group@meta.data$'SubClust.ID+NE')[grep("^MylImm",as.character(sc10x.Group@meta.data$'SubClust.ID+NE'))]))))
 
 if (opt$ne==TRUE){
-  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID+NE')[5:6,],file=paste0("./analysis/",opt$g,"/global/table/Table.SubClust.ID+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID+NE'),file=paste0("./analysis/",opt$g,"/global/table/Table.SubClust.ID+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
   write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.SubClust.ID+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID+NE')[1:4,],file=paste0("./analysis/",opt$g,"/global/table/Table.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 } else {
-  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[5:6,],file=paste0("./analysis/",opt$g,"/global/table/Table.SubClust.ID.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.SubClust.ID.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[1:4,],file=paste0("./analysis/",opt$g,"/global/table/Table.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-  write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID'),file=paste0("./analysis/",opt$g,"/global/table/Table.SubClust.ID.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID'),1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.SubClust.ID.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 }