From c6d84916144990302454ecd66ea7027efe56e471 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 23 May 2018 09:20:49 -0500
Subject: [PATCH] Fix MergeSubClusts to handle Lineage ? pops as St
---
r.scripts/sc_MergeSubClust.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc_MergeSubClust.R b/r.scripts/sc_MergeSubClust.R
index 3498adf..8d4e32e 100755
--- a/r.scripts/sc_MergeSubClust.R
+++ b/r.scripts/sc_MergeSubClust.R
@@ -45,7 +45,7 @@ Epi.cell <- names(sc10x.Group@ident[sc10x.Group@ident=="Epi"])
St.cell <- c(names(sc10x.Group@ident[sc10x.Group@ident=="St"]),names(sc10x.Group@ident[sc10x.Group@ident=="?"]))
sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Epi.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$Epi.res",opt.episubclust$r,"[sc10x.Group@ident=='Epi']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='St']"))))
+sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=c(eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='St']"))),eval(parse(text=paste0("sc10x.Group@meta.data$St.res",opt.stsubclust$r,"[sc10x.Group@ident=='?']")))))
sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("SubClust.res",opt$r))
postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Global.Merge.res.eps"))
plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
@@ -56,7 +56,7 @@ dev.off()
sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Epi.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$Epi.sub.",opt$e,"[sc10x.Group@ident=='Epi']"))))
-sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='St']"))))
+sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=St.cell,ident.use=c(eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='St']"))),eval(parse(text=paste0("sc10x.Group@meta.data$St.sub.",opt$s,"[sc10x.Group@ident=='?']")))))
sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c(
unique(as.character(sc10x.Group@ident)[grep("^Epi",as.character(sc10x.Group@ident))]),
unique(as.character(sc10x.Group@ident)[grep("^BE",as.character(sc10x.Group@ident))]),
--
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