From becb0f9985b4885d5f9eda4ceefc3d4d595fe26c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 28 Sep 2018 12:20:49 -0500
Subject: [PATCH] Make Lin identity with St+Unknown merge and diy figs
---
r.scripts/sc-TissueMapper_RUN.Pd.R | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index b6c3272..63b7f51 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -331,6 +331,10 @@ sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws_St.go",i.2="NE",nm=
sc10x.Epi <- scMerge(sc10x.Epi,sc10x.Epi,sc10x.Epi.NE,i.1="Epi.dws.sub",i.2="NE",nm="Epi.dws.sub_NE")
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
+sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[sc10x@ident %in% c("St","Unknown")]),ident.use="St")
+sc10x <- StashIdent(object=sc10x,save.name="mLin")
+
gene.orthog <- read.delim("./genesets/Ensemble.mus-hum.txt")
gene.set1 <- read_csv("./genesets/SupTab3_Consensus_Sigs.csv",skip=6)
gene.set2 <- as.data.frame(gene.set1$Basal[!is.na(gene.set1$Basal)])
@@ -478,6 +482,7 @@ for (i in ls(pattern="^genes.deg")){
}
sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D")
+sctSNECustCol(sc10x,i="mLin",bl="Epi",rd="St",file="D")
sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"),file="D")
sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="",file="D")
sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"),file="D")
@@ -492,6 +497,7 @@ sctSNEbwCol(sc10x.St,i="St.go",file="St",files="D")
for (g in c("Epi","St","Unknown")){
sctSNEHighlight(sc10x,i="Lin",g=g,file="D")
}
+sctSNEHighlight(sc10x,i="mLin",g=c("St"),file="D")
for (g in c("BE","LE","OE1","OE2")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D")
sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g,file="D")
--
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