Add no downsampling (NA) as an option for sc_PC.Score.Stress.R

r.scripts/sc_PC.Score.Stress.R

@@ -90,7 +90,11 @@ plot(plot)
 dev.off()
 
 #subsample all cells (+Stress) to better visualize their clustering
-rnd <- sample(1:ncol(sc10x.Group@data),opt$sv)
+if (!is.na(opt$s)){
+  rnd <- sample(1:ncol(sc10x.Group@data),opt$sv)
+} else {
+  rnd <- 1:ncol(sc10x.Group@data)
+}
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=sc10x.Group@data@Dimnames[[2]][rnd],ident.use="sample")
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=clusterCut,ident.use="sample")
 sc10x.Group.sample <- SubsetData(object=sc10x.Group,ident.use="sample")