From af6cb76197f29c6a4446b6b737cdd10982526ef5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 16 Feb 2020 21:29:35 -0600
Subject: [PATCH] Change singler to res 5 and fine

---
 r.scripts/SingleR.R | 33 +++++++++++++++++++--------------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/r.scripts/SingleR.R b/r.scripts/SingleR.R
index e623290..ba45a84 100644
--- a/r.scripts/SingleR.R
+++ b/r.scripts/SingleR.R
@@ -68,22 +68,27 @@ lin.se <- lin.se[common,]
 sc10x.se <- sc10x.se[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))
-sc10x$lin <- singler.lin$labels[match(sc10x.se$integrated_snn_res.0.5,singler.lin@rownames)]
+singler.lin <- SingleR(sc10x.se,ref=lin.se,method="cluster",clusters=sc10x.se$integrated_snn_res.5,labels=lin.se$label.fine,BPPARAM=MulticoreParam(workers=10))
+sc10x$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$label.main,BPPARAM=MulticoreParam(workers=10))
 #sc10x$lin <- singler.lin$labels
-if (opt$s == "hu"){
-  sc10x$lin[sc10x$lin %in% 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+")] <- "Leu"
-  sc10x$lin[sc10x$lin %in% c("Endothelial_cells","Erythroblast","Platelets")] <- "Endo"
-  sc10x$lin[sc10x$lin %in% c("Smooth_muscle_cells","Fibroblasts","Chondrocytes","Osteoblasts","MSC","Tissue_stem_cells")] <- "FMSt"
-  sc10x$lin[sc10x$lin %in% c("Epithelial_cells","Keratinocytes","Neuroepithelial_cell")] <- "Epi"
-} else if (opt$s == "mu"){
-  sc10x$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$lin %in% c("Endothelial cells")] <- "Endo"
-  sc10x$lin[sc10x$lin %in% c("Stromal cells","Fibroblasts")] <- "FMSt"
-  sc10x$lin[sc10x$lin %in% c("Epithelial cells")] <- "Epi"
-}
-#DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
+sc10x$lin[sc10x$lin %in% unique(lin.se@colData[lin.se@colData[,"label.main"] %in% c(
+  c("DC","B_cell","Neutrophil","T_cells","Monocyte","Macrophage","NK_cell","Neutrophils","CMP","GMP","MEP","Myelocyte","Pre-B_cell_CD34-","Pro-B_cell_CD34+","Pro-Myelocyte","HSC_-G-CSF","HSC_CD34+"),
+  c("Macrophages","Monocytes","B cells","DC","Eosinophils","Neutrophils","T cells","ILC","NK cells","Basophils","Mast cells","Tgd","NKT","B cells, pro","Microglia")
+  ),c("label.main","label.fine")])$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")
 
 Idents(sc10x) <- "lin"
 sc10x.epi <- subset(sc10x,idents="Epi")
-- 
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