Commit 8c701841 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Subcluster Epi and FMSt

parent e62a7dde
......@@ -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)
......
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