Commit d8e3c4e2 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add back Epi sub labels to full seurat object

parent 0f7116a9
load("./genesets/scDWS.250.rda")
load("./genesets/cibersort.rda")
singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="RNA"), annot = NULL, "huBl", min.genes = 0,
singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="SCT"), annot = NULL, "PdPbPc_deep", min.genes = 0,
technology = "10X", species = "Human", citation = "",
ref.list = list(scDWS.250), normalize.gene.length = F, variable.genes = "de",
fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = F,
......@@ -94,7 +94,7 @@ for (i in c("epi","fmst","st","leu")){
dev.off()
}
singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="RNA"), annot = NULL, "huBl", min.genes = 0,
singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="SCT"), annot = NULL, "PdPbPc_deep", min.genes = 0,
technology = "10X", species = "Human", citation = "",
ref.list = list(cibersort), normalize.gene.length = F, variable.genes = "de",
fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T,
......@@ -112,7 +112,13 @@ postscript(paste0("./analysis/vis/singler/UMAP_leu.eps"))
print(plot)
dev.off()
Idents(sc10x,cells=cells.epi) <- "Epi"
#Idents(sc10x,cells=cells.epi) <- "Epi"
Idents(sc10x,cells=cells.be) <- "BE"
Idents(sc10x,cells=cells.le) <- "LE"
Idents(sc10x,cells=cells.hillock) <- "Hillock"
Idents(sc10x,cells=cells.club) <- "Club"
Idents(sc10x,cells=cells.ne) <- "NE"
#Idents(sc10x,cells=cells.fmst) <- "FMSt"
Idents(sc10x,cells=cells.fib) <- "Fib"
Idents(sc10x,cells=cells.sm) <- "SM"
Idents(sc10x,cells=cells.endo) <- "Endo"
......
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