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plot_figure.R
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plot_figure.R
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plot_figure=function(gene,dataset){
setwd("/Users/TK/LRZ Sync+Share/Share_Bioinfo_Korn (Gildas Lepennetier)/2020.01.28_ScRNAseq_i-stream_vs_m-stream_3prime-5prime-combined")
require(Seurat)
require(ggplot2)
#"3-prime" # OR "5-prime" "combined5+3"
if(dataset=="3-prime"){GEX=readRDS("GEX_3.Rds");NAMETAG="_3prime"}
if(dataset=="5-prime"){GEX=readRDS("GEX_5.Rds");NAMETAG="_5prime"}
if(dataset=="combined5+3"){GEX=readRDS("GEX_combined5+3.Rds");NAMETAG="_Combined5+3"}
#check that the gene exists
if( ! length(grep( pattern = gene, x = rownames( GEX ), ignore.case = TRUE, value = TRUE)) >= 1 ){
print("Error: gene was not found, please check the name!")
return()
}else
OUTDIR=paste0("plots_Expression",NAMETAG,"/")
dir.create(OUTDIR,showWarnings=F)
FEATURE=gene
PLOT=FeaturePlot(GEX,features=FEATURE,pt.size=3,order=TRUE) +
theme(axis.line = element_line(size=1),
text = element_text(size = 18), #this is for the legend
axis.text = element_text(size = 26),
axis.ticks = element_line(size=1))
OUTNAME=paste0(OUTDIR,FEATURE,NAMETAG,".pdf");pdf(OUTNAME,width=10,height=10);print(PLOT);dev.off();print(paste("saved:",OUTNAME))
Idents(GEX) <- "stream"
PLOT=VlnPlot(GEX,features=FEATURE,log=TRUE,pt.size = 0) + #slot = "counts",
theme(axis.line = element_line(size=1),
text = element_text(size = 26),
axis.text = element_text(size = 26),
axis.title.x = element_blank(),
axis.ticks = element_line(size=1),
legend.position = 'none') #+ scale_y_continuous(limits = c(0, NA))
OUTNAME=paste0(OUTDIR,FEATURE,NAMETAG,"_Vplot_stream.pdf");pdf(OUTNAME,width=10,height=10);print(PLOT);dev.off();print(paste("saved:",OUTNAME))
Idents(GEX) <- "group"
PLOT=VlnPlot(GEX,features=FEATURE,log=TRUE,pt.size = 0) + #slot = "counts",
theme(axis.line = element_line(size=1),
text = element_text(size = 26),
axis.text = element_text(size = 26),
axis.title.x = element_blank(),
axis.ticks = element_line(size=1),
legend.position = 'none') #+ scale_y_continuous(limits = c(0, NA))
OUTNAME=paste0(OUTDIR,FEATURE,NAMETAG,"_Vplot_group.pdf");pdf(OUTNAME,width=10,height=10);print(PLOT);dev.off();print(paste("saved:",OUTNAME))
}