Up lin id res to 2

r.scripts/sc-TissueMapper_ID.R

@@ -85,7 +85,7 @@ pop.epi <- pop.epi[common,]
 pop.st <- pop.st[common,]
 rm(common)
 
-singler.lin <- SingleR(sc10x.se,ref=list(imm=imm,pop.epi=pop.epi,pop.st=pop.st),method="cluster",clusters=sc10x.se$integrated_snn_res.1,labels=list(imm=imm$label.main,pop.epi=pop.epi$label.fine,pop.st=pop.st$label.fine),BPPARAM=BiocParallel::MulticoreParam(workers=20))
+singler.lin <- SingleR(sc10x.se,ref=list(imm=imm,pop.epi=pop.epi,pop.st=pop.st),method="cluster",clusters=sc10x.se$integrated_snn_res.2,labels=list(imm=imm$label.main,pop.epi=pop.epi$label.fine,pop.st=pop.st$label.fine),BPPARAM=BiocParallel::MulticoreParam(workers=20))
 labs <- singler.lin$labels
 if (opt$s == "hu") {
   labs[labs %in% c("BE","LE","Hillock","Club")] <- "Epi"
@@ -98,7 +98,7 @@ if (opt$s == "hu") {
   labs[labs %in% c("Endothelial cells (LEC.CFA)","Endothelial cells (LEC)","Endothelial cells (BEC)")] <- "Endo"
   labs[labs %in% c("Macrophages","Monocytes","B cells","DC","Eosinophils","Neutrophils","T cells","ILC","NK cells","Basophils","Mast cells","Stem cells","Tgd","NKT","B cells, pro")] <- "Leu"
 }
-sc10x$lin <- labs[match(sc10x.se$integrated_snn_res.1,singler.lin@rownames)]
+sc10x$lin <- labs[match(sc10x.se$integrated_snn_res.2,singler.lin@rownames)]
 rm(labs)
 DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")