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Commit eef2df90 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix sc_QuSAGE_UKSubClust.R spelling error

parent 819df513
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...@@ -290,7 +290,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster ...@@ -290,7 +290,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster
sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage") sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("res",opt$r)) sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("res",opt$r))
sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=names(sc10x.Group.UK@ident),ident.use=paste0("UK",as.character(sc10x.Group.UK@ident))) sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=names(sc10x.Group.UK@ident),ident.use=paste0("UK",as.character(sc10x.Group.UK@ident)))
sc10x.Group <- UKashIdent(object=sc10x.Group,save.name=paste0("UK.res",opt$r)) sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("UK.res",opt$r))
postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Global.UK.res",opt$r,".eps")) postscript(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Global.UK.res",opt$r,".eps"))
plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE) plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20)) plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
...@@ -459,7 +459,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster ...@@ -459,7 +459,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster
} }
clust.order <- c(clust.order,as.character(levels(sc10x.Group.UK@ident))[!(as.character(levels(sc10x.Group.UK@ident)) %in% clust.order)]) clust.order <- c(clust.order,as.character(levels(sc10x.Group.UK@ident))[!(as.character(levels(sc10x.Group.UK@ident)) %in% clust.order)])
sc10x.Group.UK@ident <- factor(sc10x.Group.UK@ident,levels=clust.order) sc10x.Group.UK@ident <- factor(sc10x.Group.UK@ident,levels=clust.order)
sc10x.Group.UK <- UKashIdent(object=sc10x.Group.UK,save.name=paste0("UK.sub.",k)) sc10x.Group.UK <- StashIdent(object=sc10x.Group.UK,save.name=paste0("UK.sub.",k))
rm(clust.order) rm(clust.order)
rm(Ident) rm(Ident)
} }
...@@ -467,7 +467,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster ...@@ -467,7 +467,7 @@ if (file.exists(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".UKSubcluster
sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage") sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("UK.sub.",i)) sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("UK.sub.",i))
sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=names(sc10x.Group.UK@ident),ident.use=paste0("UK",as.character(sc10x.Group.UK@ident))) sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=names(sc10x.Group.UK@ident),ident.use=paste0("UK",as.character(sc10x.Group.UK@ident)))
sc10x.Group <- UKashIdent(object=sc10x.Group,save.name=paste0("UK.sub.",i)) sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("UK.sub.",i))
sc10x.Group <- SetAllIdent(object=sc10x.Group,id=paste0("UK.sub.",i)) sc10x.Group <- SetAllIdent(object=sc10x.Group,id=paste0("UK.sub.",i))
sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("UK.sub.",i)) sc10x.Group.UK <- SetAllIdent(object=sc10x.Group.UK,id=paste0("UK.sub.",i))
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