Commit 8ca3e573 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Merge branch 'FACS' into 'develop'

Merge FACS into Develop

See merge request sc-TissueMapper_Pr!1
parents c88d11c4 e2ef9276
#!/bin/bash
#SBATCH --job-name R_FullAnalysis
#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
#SBATCH -o job_%j.out
#SBATCH -e job_%j.out
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
module load R/3.4.1-gccmkl
Rscript ../r.scripts/sc-TissueMapper_RUN.D17_FACS.R
#!/bin/bash
#SBATCH --job-name R_FullAnalysis
#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
#SBATCH -o job_%j.out
#SBATCH -e job_%j.out
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
module load R/3.4.1-gccmkl
Rscript ../r.scripts/sc-TissueMapper_RUN.D27_FACS.R
......@@ -1181,7 +1181,7 @@ sctSNECustCol <- function(sc10x,i,bl,rd,file){
sctSNEbwCol <- function(sc10x,i,file,files){
sc10x <- SetAllIdent(object=sc10x,id=i)
sc10x@ident <- factor(sc10x@ident,levels=c("Epi","BE","LE","OE1","OE_SCGB","OE2","OE_KRT13","St","Fib","SM","Endo","Leu","Unknown",1:10))
sc10x@ident <- factor(sc10x@ident,levels=c("Epi","BE","LE","OE1","OE_SCGB","OE2","OE_KRT13","St","Fib","SM","Endo","Leu","Unknown",1:50))
postscript(paste0("./analysis/diy/tSNE_",files,".",file,"_",i,".bwCol.eps"))
plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=colorRampPalette(c("white","black"))(length(unique(sc10x@ident))+2)[3:(length(unique(sc10x@ident))+2)])
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
......
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