Subcluster Epi and FMSt

r.scripts/sc-TissueMapper_RUN.PdPbPc.cca.R

@@ -237,14 +237,31 @@ genes.leu.l[nrow(genes.leu.l)+1,] <- list("FCN1","Neutrophils",0)
   rm(results)
   rm(gene.set)
   
-  res.leu <- 1
+  res.pop <- 1
 
   sc10x <- SetAllIdent(object=sc10x,id="Pop")
+
+  try({
+    sc10x.Epi <- scSubset(sc10x,i="Pop",g="Epi")
+    sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
+    sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name=paste0("old.res",opt$res.poststress))
+    sc10x.Epi <- scCluster(sc10x.Epi,pc.use=opt$acca,res.use=res.pop,folder=paste0("epi/",i),red="cca.aligned")
+    assign(paste0("sc10x.Epi.",i,".analized"),sc10x.Epi)
+  })
+
+  try({
+    sc10x.FMSt <- scSubset(sc10x,i="Pop",g="FMSt")
+    sc10x.FMSt <- SetAllIdent(object=sc10x.FMSt,id=paste0("res",opt$res.poststress))
+    sc10x.FMSt <- StashIdent(object=sc10x.FMSt,save.name=paste0("old.res",opt$res.poststress))
+    sc10x.FMSt <- scCluster(sc10x.FMSt,pc.use=opt$acca,res.use=res.pop,folder=paste0("st/",i),red="cca.aligned")
+    assign(paste0("sc10x.FMSt.",i,".analized"),sc10x.FMSt)
+  })
+
   try({
     sc10x.Lymphoid <- scSubset(sc10x,i="Pop",g="Lymphoid")
     sc10x.Lymphoid <- SetAllIdent(object=sc10x.Lymphoid,id=paste0("res",opt$res.poststress))
     sc10x.Lymphoid <- StashIdent(object=sc10x.Lymphoid,save.name=paste0("old.res",opt$res.poststress))
-    sc10x.Lymphoid <- scCluster(sc10x.Lymphoid,pc.use=opt$acca,res.use=res.leu,folder=paste0("lymphoid/",i),red="cca.aligned")
+    sc10x.Lymphoid <- scCluster(sc10x.Lymphoid,pc.use=opt$acca,res.use=res.pop,folder=paste0("lymphoid/",i),red="cca.aligned")
     assign(paste0("sc10x.Lymphoid.",i,".analized"),sc10x.Lymphoid)
   })
 
@@ -252,7 +269,7 @@ genes.leu.l[nrow(genes.leu.l)+1,] <- list("FCN1","Neutrophils",0)
     sc10x.Myeloid <- scSubset(sc10x,i="Pop",g="Myeloid")
     sc10x.Myeloid <- SetAllIdent(object=sc10x.Myeloid,id=paste0("res",opt$res.poststress))
     sc10x.Myeloid <- StashIdent(object=sc10x.Myeloid,save.name=paste0("old.res",opt$res.poststress))
-    sc10x.Myeloid <- scCluster(sc10x.Myeloid,pc.use=opt$acca,res.use=res.leu,folder=paste0("myeloid/",i),red="cca.aligned")
+    sc10x.Myeloid <- scCluster(sc10x.Myeloid,pc.use=opt$acca,res.use=res.pop,folder=paste0("myeloid/",i),red="cca.aligned")
     assign(paste0("sc10x.Myeloid.",i,".analized"),sc10x.Myeloid)
   })
   
@@ -261,6 +278,8 @@ genes.leu.l[nrow(genes.leu.l)+1,] <- list("FCN1","Neutrophils",0)
   assign(paste0("results.clust.Lin.id.",i),results.clust.Lin.id)
 
   rm(sc10x)
+  rm(sc10x.Epi)
+  rm(sc10x.FMSt)
   rm(sc10x.Lymphoid)
   rm(sc10x.Myeloid)
   rm(sc10x.Leu)