Commit c8ee0098 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Use res 5 for lin in hu mu singelr

parent af6cb761
...@@ -88,7 +88,7 @@ sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in ...@@ -88,7 +88,7 @@ sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in
c("Epithelial_cells","Keratinocytes","Neuroepithelial_cell"), c("Epithelial_cells","Keratinocytes","Neuroepithelial_cell"),
c("Epithelial cells") c("Epithelial cells")
),c("label.main","label.fine")])$label.fine] <- "Epi" ),c("label.main","label.fine")])$label.fine] <- "Epi"
DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none") #DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
Idents(sc10x) <- "lin" Idents(sc10x) <- "lin"
sc10x.epi <- subset(sc10x,idents="Epi") sc10x.epi <- subset(sc10x,idents="Epi")
......
...@@ -77,14 +77,26 @@ lin.se <- lin.se[common,] ...@@ -77,14 +77,26 @@ lin.se <- lin.se[common,]
sc10x.se <- sc10x.se[common,] sc10x.se <- sc10x.se[common,]
rm(common) rm(common)
singler.lin <- SingleR(sc10x.se,ref=lin.se,method="cluster",clusters=sc10x.se$integrated_snn_res.0.5,labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10)) singler.lin <- SingleR(sc10x.se,ref=lin.se,method="cluster",clusters=sc10x.se$integrated_snn_res.5,labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10))
sc10x$lin <- singler.lin$labels[match(sc10x.se$integrated_snn_res.0.5,singler.lin@rownames)] sc10x$lin <- singler.lin$labels[match(sc10x.se$integrated_snn_res.5,singler.lin@rownames)]
#singler.lin <- SingleR(sc10x.se,ref=lin.se,method="single",labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10)) #singler.lin <- SingleR(sc10x.se,ref=lin.se,method="single",labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10))
#sc10x$lin <- singler.lin$labels #sc10x$lin <- singler.lin$labels
sc10x$lin[sc10x$lin %in% c("Macrophages","Monocytes","B cells","DC","Eosinophils","Neutrophils","T cells","ILC","NK cells","Basophils","Mast cells","Tgd","NKT","B cells, pro","Microglia")] <- "Leu" sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in% c(
sc10x$lin[sc10x$lin %in% c("Endothelial cells")] <- "Endo" c("DC","B_cell","Neutrophil","T_cells","Monocyte","Macrophage","NK_cell","Neutrophils","CMP","GMP","MEP","Myelocyte","Pre-B_cell_CD34-","Pro-B_cell_CD34+","Pro-Myelocyte","HSC_-G-CSF","HSC_CD34+"),
sc10x$lin[sc10x$lin %in% c("Stromal cells","Fibroblasts")] <- "FMSt" c("Macrophages","Monocytes","B cells","DC","Eosinophils","Neutrophils","T cells","ILC","NK cells","Basophils","Mast cells","Tgd","NKT","B cells, pro","Microglia")
sc10x$lin[sc10x$lin %in% c("Epithelial cells")] <- "Epi" ),c("label.main","label.fine")])$label.fine] <- "Leu"
sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in% c(
c("Endothelial_cells","Erythroblast","Platelets"),
c("Endothelial cells")
),c("label.main","label.fine")])$label.fine] <- "Endo"
sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in% c(
c("Smooth_muscle_cells","Fibroblasts","Chondrocytes","Osteoblasts","MSC","Tissue_stem_cells"),
c("Stromal cells","Fibroblasts")
),c("label.main","label.fine")])$label.fine] <- "FMSt"
sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in% c(
c("Epithelial_cells","Keratinocytes","Neuroepithelial_cell"),
c("Epithelial cells")
),c("label.main","label.fine")])$label.fine] <- "Epi"
#DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none") #DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
Idents(sc10x) <- "lin" Idents(sc10x) <- "lin"
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment