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Commit c9536e9e authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Update QuSAGE codes to correlate to DWS sc Pop DEGs

parent e4a117e1
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......@@ -11,6 +11,7 @@ option_list=list(
make_option("--p",action="store",default="Pr",type='character',help="Project Name"),
make_option("--g",action="store",default="ALL",type='character',help="Group To Analyze"),
make_option("--r",action="store",default=0.1,type='numeric',help="Resolution"),
make_option("--gs",action="store",default="bulk",type='character',help="Source of geneset"),
make_option("--st",action="store",default=TRUE,type='logical',help="Analyze Data With Stress Pops Removed?"),
make_option("--s",action="store",default=20000,type='integer',help="Number Of Cells To Downsample To")
)
......@@ -73,14 +74,25 @@ for (i in 1:Number.Clusters){
cC[i] <- paste0("Cluster_",i,"-REST")
}
rm(labels)
gene.set2 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "St"
gene.set <- c(gene.set2)
gene.set2 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "Epi"
gene.set <- c(gene.set,gene.set2)
if (opt$gs=="bulk"){
gene.set2 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "St"
gene.set <- c(gene.set2)
gene.set2 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "Epi"
gene.set <- c(gene.set,gene.set2)
} else if (opt$gs=="sc"){
gene.set2 <- read_delim("./genesets/DEG_St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2 <- as.list(gene.set2[,2])
names(gene.set2) <- "St"
gene.set <- c(gene.set2)
gene.set2 <- read_delim("./genesets/DEG_Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2 <- as.list(gene.set2[,2])
names(gene.set2) <- "Epi"
gene.set <- c(gene.set,gene.set2)
}
rm(gene.set2)
for (i in 1:Number.Clusters){
assign(paste0("qs.results.",i),qusage(eset,unlist(C[i]),unlist(cC[i]),gene.set))
......
......@@ -17,7 +17,8 @@ option_list=list(
make_option("--dws",action="store",default=TRUE,type='logical',help="Correlate to DWS Epi?"),
make_option("--lgea",action="store",default=TRUE,type='logical',help="Correlate to LGEA Epi?"),
make_option("--c2",action="store",default=FALSE,type='logical',help="Correlate to c2 KEGG?"),
make_option("--c5",action="store",default=FALSE,type='logical',help="Correlate to c5 BP?")
make_option("--c5",action="store",default=FALSE,type='logical',help="Correlate to c5 BP?"),
make_option("--sc",action="store",default=FALSE,type='logical',help="Correlate to sc?")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
......@@ -89,6 +90,9 @@ if (opt$dws==TRUE){
if (opt$lgea==TRUE){
sets=c(sets,"lgea")
}
if (opt$sc==TRUE){
sets=c(sets,"sc")
}
gene.set2 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
......@@ -126,6 +130,26 @@ rm(gene.set2)
gene.set.c2 <- read.gmt("./genesets/c2.cp.kegg.v6.1.symbols.gmt")
gene.set.c5 <- read.gmt("./genesets/c5.bp.v6.1.symbols.gmt")
if (opt$sc==TRUE){
gene.set2.sc <- read_delim("./genesets/DEG_BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "BE"
gene.set.sc <- c(gene.set2.sc)
gene.set2.sc <- read_delim("./genesets/DEG_LE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "LE"
gene.set.sc <- c(gene.set.sc,gene.set2.sc)
gene.set2.sc <- read_delim("./genesets/DEG_OE1.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "OE_PSCA"
gene.set.sc <- c(gene.set.sc,gene.set2.sc)
gene.set2.sc <- read_delim("./genesets/DEG_OE2.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "OE_KRT13"
gene.set.sc <- c(gene.set.sc,gene.set2.sc)
rm(gene.set2.sc)
}
#run QuSAGE
for (i in 1:Number.Clusters){
if (opt$dws==TRUE){
......@@ -140,6 +164,9 @@ for (i in 1:Number.Clusters){
if (opt$c5==TRUE){
assign(paste0("qs.results.epi.c5.",i),qusage(eset,unlist(C[i]),unlist(cC[i]),gene.set.c5))
}
if (opt$sc==TRUE){
assign(paste0("qs.results.epi.sc.",i),qusage(eset,unlist(C[i]),unlist(cC[i]),gene.set.sc))
}
}
rm(eset)
rm(C)
......@@ -174,6 +201,20 @@ if (opt$lgea==TRUE){
if (max(qs$path.PDF)>max.y.rg.lgea){
max.y.rg.lgea <- max(qs$path.PDF)
}}}
if (opt$sc==TRUE){
max.x.rg.sc <- 0
min.x.rg.sc <- 0
max.y.rg.sc <- 0
for (i in 1:Number.Clusters){
qs <- get(paste0("qs.results.epi.sc.",i))
if (max(qs$path.mean)>max.x.rg.sc){
max.x.rg.sc <- max(qs$path.mean)
if (min(qs$path.mean)<min.x.rg.sc){
min.x.rg.sc <- min(qs$path.mean)
}}
if (max(qs$path.PDF)>max.y.rg.sc){
max.y.rg.sc <- max(qs$path.PDF)
}}}
for (i in 1:Number.Clusters){
if (opt$dws==TRUE){
qs <- get(paste0("qs.results.epi.dws.",i))
......@@ -208,6 +249,13 @@ for (i in 1:Number.Clusters){
tab <- tab[tab$FDR<0.05,]
tab <- tab[order(-tab[,2]),]
write.table(tab,file=paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_Epi_",i,".Table.c5.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
}
if (opt$sc==TRUE){
qs <- get(paste0("qs.results.epi.sc.",i))
postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_Epi_",i,".sc.eps"))
plotDensityCurves(qs,path.index=1:3,col=1:numPathways(qs),main=paste0("Cluster ",i),xlim=c(min.x.rg.sc-0.05,max.x.rg.sc+0.05),ylim=c(0,50*ceiling(max.y.rg.sc/50)),xlab="Gene Set Activation",lwd=2,cex.main=2.5)
legend("topright",legend=c("BE","LE","OE_PSCA","OE_KRT13"),lty=1,col=1:numPathways(qs),lwd=1,cex=2,ncol=1,bty="n",pt.cex=1)
dev.off()
}}
rm(max.x.rg.dws)
rm(min.x.rg.dws)
......@@ -215,6 +263,9 @@ rm(max.y.rg.dws)
rm(max.x.rg.lgea)
rm(min.x.rg.lgea)
rm(max.y.rg.lgea)
rm(max.x.rg.sc)
rm(min.x.rg.sc)
rm(max.y.rg.sc)
#generate ID tables
rm(qs.Cor.table)
......@@ -407,6 +458,77 @@ for (k in sets){
sc10x.Group.Epi <- SetAllIdent(object=sc10x.Group.Epi,id=paste0("res",opt$r))
sc10x.Group.Epi@ident <- plyr::mapvalues(x=sc10x.Group.Epi@ident,from=1:Number.Clusters,to=merge.cluster)
clust.order <- c(grep("BC",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE),grep("AT2",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE),grep("CGC",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE))
} else if (k=="sc"){
tryCatch({
UK <- Ident[,"?"]
UK <- UK[UK>0]
UK <- as.integer(names(UK))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
BE_sc <- Ident[,"BE"]
BE_sc <- BE_sc[BE_sc>0]
BE_sc <- as.integer(names(BE_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
LE_sc <- Ident[,"LE"]
LE_sc <- LE_sc[LE_sc>0]
LE_sc <- as.integer(names(LE_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
OE_PSCA <- Ident[,"OE_PSCA"]
OE_PSCA <- OE_PSCA[OE_PSCA>0]
OE_PSCA <- as.integer(names(OE_PSCA))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
OE_KRT13 <- Ident[,"OE_KRT13"]
OE_KRT13 <- OE_KRT13[OE_KRT13>0]
OE_KRT13 <- as.integer(names(OE_KRT13))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
merge.cluster <- NULL
for (i in 1:Number.Clusters){
if (exists("UK")==TRUE){
for (j in 1:length(UK)){
if (UK[j]==i){
if (length(UK)>1){
merge.cluster <- c(merge.cluster,paste0("?",j))
} else {
merge.cluster <- c(merge.cluster,"?")
}}}}
if (exists("BE_sc")==TRUE){
for (j in 1:length(BE_sc)){
if (BE_sc[j]==i){
if (length(BE_sc)>1){
merge.cluster <- c(merge.cluster,paste0("BE",j))
} else {
merge.cluster <- c(merge.cluster,"BE")
}}}}
if (exists("LE_sc")==TRUE){
for (j in 1:length(LE_sc)){
if (LE_sc[j]==i){
if (length(LE_sc)>1){
merge.cluster <- c(merge.cluster,paste0("LE",j))
} else {
merge.cluster <- c(merge.cluster,"LE")
}}}}
if (exists("OE_PSCA")==TRUE){
for (j in 1:length(OE_PSCA)){
if (OE_PSCA[j]==i){
if (length(OE_PSCA)>1){
merge.cluster <- c(merge.cluster,paste0("OE_PSCA",j))
} else {
merge.cluster <- c(merge.cluster,"OE_PSCA")
}}}}
if (exists("OE_KRT13")==TRUE){
for (j in 1:length(OE_KRT13)){
if (OE_KRT13[j]==i){
if (length(OE_KRT13)>1){
merge.cluster <- c(merge.cluster,paste0("OE_KRT13",j))
} else {
merge.cluster <- c(merge.cluster,"OE_KRT13")
}}}}}
sc10x.Group.Epi <- SetAllIdent(object=sc10x.Group.Epi,id=paste0("res",opt$r))
sc10x.Group.Epi@ident <- plyr::mapvalues(x=sc10x.Group.Epi@ident,from=1:Number.Clusters,to=merge.cluster)
clust.order <- c(grep("BE",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE),grep("LE",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE),grep("OE_PSCA",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE),grep("OE_KRT13",as.character(levels(sc10x.Group.Epi@ident)),value=TRUE))
}
clust.order <- c(clust.order,as.character(levels(sc10x.Group.Epi@ident))[!(as.character(levels(sc10x.Group.Epi@ident)) %in% clust.order)])
sc10x.Group.Epi@ident <- factor(sc10x.Group.Epi@ident,levels=clust.order)
......@@ -434,12 +556,17 @@ for (i in sets){
dev.off()
}
rm(plot)
rm(UK)
rm(BE)
rm(LE)
rm(OE)
rm(BC)
rm(AT2)
rm(CGC)
rm(BE_sc)
rm(LE_sc)
rm(OE_PSCA)
rm(OE_KRT13)
#make generic variables of run specific variables
for (i in sets){
......
......@@ -17,7 +17,8 @@ option_list=list(
make_option("--go",action="store",default=TRUE,type='logical',help="Correlate to GO St?"),
make_option("--lgea",action="store",default=TRUE,type='logical',help="Correlate to LGEA St?"),
make_option("--c2",action="store",default=FALSE,type='logical',help="Correlate to c2?"),
make_option("--c5",action="store",default=FALSE,type='logical',help="Correlate to c5?")
make_option("--c5",action="store",default=FALSE,type='logical',help="Correlate to c5?"),
make_option("--sc",action="store",default=FALSE,type='logical',help="Correlate to sc?")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
......@@ -87,6 +88,9 @@ if (opt$go==TRUE){
if (opt$lgea==TRUE){
sets=c(sets,"lgea")
}
if (opt$sc==TRUE){
sets=c(sets,"sc")
}
gene.set2 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2 <- as.list(gene.set2[-1,])
......@@ -99,6 +103,10 @@ gene.set <- c(gene.set,gene.set2)
gene.set2 <- read_delim("./genesets/DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2 <- as.list(gene.set2[-1,])
names(gene.set2) <- "Fib"
gene.set <- c(gene.set,gene.set2)
gene.set2 <- read_delim("./genesets/DEG_C5.BP.M10124.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2 <- as.list(gene.set2[-1,])
names(gene.set2) <- "Leu"
gene.set.go <- c(gene.set,gene.set2)
rm(gene.set)
rm(gene.set2)
......@@ -136,6 +144,22 @@ rm(gene.set3)
gene.set.c2 <- read.gmt("./genesets/c2.cp.kegg.v6.1.symbols.gmt")
gene.set.c5 <- read.gmt("./genesets/c5.bp.v6.1.symbols.gmt")
if (opt$sc==TRUE){
gene.set2.sc <- read_delim("./genesets/DEG_Fib.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "Fib"
gene.set.sc <- c(gene.set2.sc)
gene.set2.sc <- read_delim("./genesets/DEG_SM.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "SM"
gene.set.sc <- c(gene.set.sc,gene.set2.sc)
gene.set2.sc <- read_delim("./genesets/DEG_Endo.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set2.sc <- as.list(gene.set2.sc[,2])
names(gene.set2.sc) <- "Endo"
gene.set.sc <- c(gene.set.sc,gene.set2.sc)
rm(gene.set2.sc)
}
#run QuSAGE
for (i in 1:Number.Clusters){
if (opt$go==TRUE){
......@@ -150,6 +174,9 @@ for (i in 1:Number.Clusters){
if (opt$c5==TRUE){
assign(paste0("qs.results.st.c5.",i),qusage(eset,unlist(C[i]),unlist(cC[i]),gene.set.c5))
}
if (opt$sc==TRUE){
assign(paste0("qs.results.st.sc.",i),qusage(eset,unlist(C[i]),unlist(cC[i]),gene.set.sc))
}
}
rm(eset)
rm(C)
......@@ -184,6 +211,20 @@ if (opt$lgea==TRUE){
if (max(qs$path.PDF)>max.y.rg.lgea){
max.y.rg.lgea <- max(qs$path.PDF)
}}}
if (opt$sc==TRUE){
max.x.rg.sc <- 0
min.x.rg.sc <- 0
max.y.rg.sc <- 0
for (i in 1:Number.Clusters){
qs <- get(paste0("qs.results.epi.sc.",i))
if (max(qs$path.mean)>max.x.rg.sc){
max.x.rg.sc <- max(qs$path.mean)
if (min(qs$path.mean)<min.x.rg.sc){
min.x.rg.sc <- min(qs$path.mean)
}}
if (max(qs$path.PDF)>max.y.rg.sc){
max.y.rg.sc <- max(qs$path.PDF)
}}}
for (i in 1:Number.Clusters){
if (opt$go==TRUE){
qs <- get(paste0("qs.results.st.go.",i))
......@@ -218,13 +259,23 @@ for (i in 1:Number.Clusters){
tab <- tab[tab$FDR<0.05,]
tab <- tab[order(-tab[,2]),]
write.table(tab,file=paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_St_",i,".Table.c5.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
}}
}
if (opt$sc==TRUE){
qs <- get(paste0("qs.results.st.sc.",i))
postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_St_",i,".sc.eps"))
plotDensityCurves(qs,path.index=1:3,col=1:numPathways(qs),main=paste0("Cluster ",i),xlim=c(min.x.rg.sc-0.05,max.x.rg.sc+0.05),ylim=c(0,50*ceiling(max.y.rg.sc/50)),xlab="Gene Set Activation",lwd=2,cex.main=2.5)
legend("topright",legend=c("BE","LE","OE_PSCA","OE_KRT13"),lty=1,col=1:numPathways(qs),lwd=1,cex=2,ncol=1,bty="n",pt.cex=1)
dev.off()
}}
rm(max.x.rg.go)
rm(min.x.rg.go)
rm(max.y.rg.go)
rm(max.x.rg.lgea)
rm(min.x.rg.lgea)
rm(max.y.rg.lgea)
rm(max.x.rg.sc)
rm(min.x.rg.sc)
rm(max.y.rg.sc)
#generate ID tables
rm(qs.Cor.table)
......@@ -356,6 +407,11 @@ for (k in sets){
Fib <- Fib[Fib>0]
Fib <- as.integer(names(Fib))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
Leu <- Ident[,"Leu"]
Leu <- Leu[Leu>0]
Leu <- as.integer(names(Leu))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
merge.cluster <- NULL
for (i in 1:Number.Clusters){
if (exists("UK")==TRUE){
......@@ -389,10 +445,18 @@ for (k in sets){
merge.cluster <- c(merge.cluster,paste0("Fib",j))
} else {
merge.cluster <- c(merge.cluster,"Fib")
}}}}}
}}}}
if (exists("Leu")==TRUE){
for (j in 1:length(Leu)){
if (Leu[j]==i){
if (length(Leu)>1){
merge.cluster <- c(merge.cluster,paste0("Leu",j))
} else {
merge.cluster <- c(merge.cluster,"Leu")
}}}}}
sc10x.Group.St <- SetAllIdent(object=sc10x.Group.St,id=paste0("res",opt$r))
sc10x.Group.St@ident <- plyr::mapvalues(x=sc10x.Group.St@ident,from=1:Number.Clusters,to=merge.cluster)
clust.order <- c(grep("Fib",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("SM",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Endo",as.character(levels(sc10x.Group.St@ident)),value=TRUE))
clust.order <- c(grep("Fib",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("SM",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Endo",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Leu",as.character(levels(sc10x.Group.St@ident)),value=TRUE))
} else if (k=="lgea"){
tryCatch({
UK <- Ident[,"?"]
......@@ -490,6 +554,77 @@ for (k in sets){
sc10x.Group.St <- SetAllIdent(object=sc10x.Group.St,id=paste0("res",opt$r))
sc10x.Group.St@ident <- plyr::mapvalues(x=sc10x.Group.St@ident,from=1:Number.Clusters,to=merge.cluster)
clust.order <- c(grep("ProlFib",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("MatFib",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("MyoFibSM",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("EndoC",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Peri",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("MylImmune",as.character(levels(sc10x.Group.St@ident)),value=TRUE))
} else if (k=="sc"){
tryCatch({
UK <- Ident[,"?"]
UK <- UK[UK>0]
UK <- as.integer(names(UK))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
Endo_sc <- Ident[,"Endo"]
Endo_sc <- Endo_sc[Endo_sc>0]
Endo_sc <- as.integer(names(Endo_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
SM_sc <- Ident[,"SM"]
SM_sc <- SM_sc[SM_sc>0]
SM_sc <- as.integer(names(SM_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
Fib_sc <- Ident[,"Fib"]
Fib_sc <- Fib_sc[Fib_sc>0]
Fib_sc <- as.integer(names(Fib_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
tryCatch({
Leu_sc <- Ident[,"Leu"]
Leu_sc <- Leu_sc[Leu_sc>0]
Leu_sc <- as.integer(names(Leu_sc))
},error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
merge.cluster <- NULL
for (i in 1:Number.Clusters){
if (exists("UK")==TRUE){
for (j in 1:length(UK)){
if (UK[j]==i){
if (length(UK)>1){
merge.cluster <- c(merge.cluster,paste0("?",j))
} else {
merge.cluster <- c(merge.cluster,"?")
}}}}
if (exists("Endo_sc")==TRUE){
for (j in 1:length(Endo_sc)){
if (Endo_sc[j]==i){
if (length(Endo_sc)>1){
merge.cluster <- c(merge.cluster,paste0("Endo",j))
} else {
merge.cluster <- c(merge.cluster,"Endo")
}}}}
if (exists("SM_sc")==TRUE){
for (j in 1:length(SM_sc)){
if (SM_sc[j]==i){
if (length(SM_sc)>1){
merge.cluster <- c(merge.cluster,paste0("SM",j))
} else {
merge.cluster <- c(merge.cluster,"SM")
}}}}
if (exists("Fib_sc")==TRUE){
for (j in 1:length(Fib_sc)){
if (Fib_sc[j]==i){
if (length(Fib_sc)>1){
merge.cluster <- c(merge.cluster,paste0("Fib",j))
} else {
merge.cluster <- c(merge.cluster,"Fib")
}}}}
if (exists("Leu_sc")==TRUE){
for (j in 1:length(Leu_sc)){
if (Leu_sc[j]==i){
if (length(Leu_sc)>1){
merge.cluster <- c(merge.cluster,paste0("Leu",j))
} else {
merge.cluster <- c(merge.cluster,"Leu")
}}}}}
sc10x.Group.St <- SetAllIdent(object=sc10x.Group.St,id=paste0("res",opt$r))
sc10x.Group.St@ident <- plyr::mapvalues(x=sc10x.Group.St@ident,from=1:Number.Clusters,to=merge.cluster)
clust.order <- c(grep("Fib",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("SM",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Endo",as.character(levels(sc10x.Group.St@ident)),value=TRUE),grep("Leu",as.character(levels(sc10x.Group.St@ident)),value=TRUE))
}
clust.order <- c(clust.order,as.character(levels(sc10x.Group.St@ident))[!(as.character(levels(sc10x.Group.St@ident)) %in% clust.order)])
sc10x.Group.St@ident <- factor(sc10x.Group.St@ident,levels=clust.order)
......@@ -519,15 +654,21 @@ for (i in sets){
dev.off()
}
rm(plot)
rm(U)
rm(Endo)
rm(SM)
rm(Fib)
rm(Leu)
rm(ProlFib)
rm(MyoFibSM)
rm(Peri)
rm(MatFib)
rm(EndoC)
rm(MylImm)
rm(Endo_sc)
rm(SM_sc)
rm(Fib_sc)
rm(Leu_sc)
#make generic variables of run specific variables
for (i in sets){
......
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