Fix lin subset if unknown present and re-tSNE St

r.scripts/sc-TissueMapper_RUN.D17_FACS.R

@@ -187,6 +187,7 @@ results.clust.Lin.id <- results[[3]]
 rm(results)
 rm(gene.set)
 
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
 sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
 if (any(levels(sc10x@ident)=="Unknown")){
   sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
@@ -215,6 +216,21 @@ plot(plot)
 dev.off()
 rm(plot)
 
+sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="pca",dims.use=1:pc.use.poststress,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/st/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+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+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/st/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+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+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
 gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set1 <- gene.set1[1]
 gene.set1 <- as.list(gene.set1)