Commit 74ac6ca5 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Up lin id res to 2

parent 6356ce6b
......@@ -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")
......
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