Change lin ID to single mode

r.scripts/sc-TissueMapper_ID.R

@@ -104,10 +104,10 @@ if (opt$s == "hu"){
   rm(lin)
 }
   
-#singler <- SingleR(sc10x.se,ref=ref,method="single",labels=labels,de.method="wilcox",BPPARAM=BiocParallel::MulticoreParam(workers=20))
-#labs <- singler$labels
-singler <- SingleR(sc10x.se,ref=ref,clusters=sc10x.se$integrated_snn_res.1,labels=labels,de.method="wilcox",BPPARAM=BiocParallel::MulticoreParam(workers=20))
-labs <- singler$labels[match(sc10x.se$integrated_snn_res.1,singler@rownames)]
+singler <- SingleR(sc10x.se,ref=ref,method="single",labels=labels,de.method="wilcox",BPPARAM=BiocParallel::MulticoreParam(workers=20))
+labs <- singler$labels
+#singler <- SingleR(sc10x.se,ref=ref,clusters=sc10x.se$integrated_snn_res.1,labels=labels,de.method="wilcox",BPPARAM=BiocParallel::MulticoreParam(workers=20))
+#labs <- singler$labels[match(sc10x.se$integrated_snn_res.1,singler@rownames)]
 sc10x$pop <- labs
 labs.raw <- labs
 labs[labs %in% c("Differentiating Basal","Proliferating Basal","Basal","Mesothelial","Alveolar Epithelial Type 2","Club","Alveolar Epithelial Type 1","Ciliated","Signaling Alveolar Epithelial Type 2","Proximal Basal","Neuroendocrine","Mucous","Ionocyte","Serous","Proximal Ciliated","Goblet")] <- "Epithelia"
@@ -209,7 +209,7 @@ if (opt$o == "pr" && opt$s == "hu") {
   singler.epi <- SingleR(sc10x.se.epi,ref=pop.epi,method="single",labels=pop.epi$label.fine,de.method="wilcox",BPPARAM=BiocParallel::MulticoreParam(workers=20))
   sc10x.epi$pop <- singler.epi$labels
   Idents(sc10x.epi) <- "pop"
-  sc10x[["pop"]][row.names(sc10x.epi[["pop"]])] <- sc10x.epi[["pop"]][,"pop"]
+  sc10x[["pop"]][row.names(sc10x.epi[["pop"]]),] <- sc10x.epi[["pop"]][,"pop"]
   #DimPlot(sc10x.epi,group.by="pop",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 } else if (opt$o == "pr" && opt$s == "mu") {
   sc10x.epi$pop <- sc10x.epi$lin
@@ -218,7 +218,6 @@ if (opt$o == "pr" && opt$s == "hu") {
 }
 
 sc10x$pop <- sc10x$lin
-
 sc10x$pop[names(sc10x.epi$pop)] <- sc10x.epi$pop
 sc10x$pop[names(sc10x.leu$pop)] <- sc10x.leu$pop
 #DimPlot(sc10x,group.by="pop",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")