fix saving bugs in stats (65e694fa) · Commits · github_fork / ZUMIs

zUMIs-stats2.R

+6 −2

Original line number	Diff line number	Diff line
		@@ -9,6 +9,8 @@ library(yaml)
		library(ggplot2)
		library(Matrix)
		library(dplyr)
		library(cowplot)

		##########################
		myYaml<-commandArgs(trailingOnly = T)
		opt <-read_yaml(myYaml)
		@@ -51,7 +53,7 @@ bg <- countBoxplot(cnt = umicounts,
		lab = medUMI)
		cp<-cowplot::plot_grid(ag,bg,ncol = 2)

		ggsave(c,filename = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".geneUMIcounts.pdf",sep=""),width = 10,height = 5)
		ggsave(cp,filename = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".geneUMIcounts.pdf",sep=""),width = 10,height = 5)
		write.table(genecounts,file = paste0(opt$out_dir,"/zUMIs_output/stats/",opt$project,".genecounts.txt"),sep="\t",row.names = F,col.names = T)
		write.table(umicounts,file = paste0(opt$out_dir,"/zUMIs_output/stats/",opt$project,".UMIcounts.txt"),sep="\t",row.names = F,col.names = T)

		@@ -66,6 +68,7 @@ typeCount <- sumstatBAM(featfiles=c(paste0(opt$out_dir,"/",opt$project,".filtere
		outfile = paste0(opt$out_dir,"/zUMIs_output/stats/",opt$project,".bc.READcounts.rds"))

		#only print per BC mapping stats if there are fewer than 200 BCs

		if(length( unique(typeCount$RG))<=200 ){
		tc<-data.frame(typeCount)
		tc$type<-factor(tc$type, levels=rev(c("Exon","Intron","Intergenic","Ambiguity","Unmapped","User")))
		@@ -82,7 +85,7 @@ if(length( unique(typeCount$RG))<=200 ){
		legend.title = element_blank())

		ggsave(p,filename = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".readspercell.pdf",sep=""),width = 10,height = 7)
		write.table(cellTotal,file = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".readspercell.txt",sep=""),sep="\t",row.names = F,col.names = T)
		write.table(tc,file = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".readspercell.txt",sep=""),sep="\t",row.names = F,col.names = T)
		}

		##### Reads per cell based on their assignment type ###3
		@@ -100,3 +103,4 @@ d<-plot_grid(cp,bar,box,ncol = 1,rel_heights = c(0.3,0.2,0.5))

		ggsave(d,filename = paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,".features.pdf",sep=""),width = 12,height = 9)

		gc()

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