17 lines
832 B
R
17 lines
832 B
R
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args <- commandArgs(TRUE)
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if(length(args)!=3){
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stop('usage:Rscript $0 <sample_prefix> <insertsize.plot from bamdst> <depth_distribution.plot from bamddst>')
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}
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sample<-args[1]
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png(paste0(sample,".png"),width=1024,height=768)
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layout(matrix(c(1,1,2,3),2,2,byrow=T))
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insert<-read.table(args[2])
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depth<-read.table(args[3])
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par(cex=1.5)
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plot(insert[,1],insert[,3],type="h",xlim=c(0,1000),col="red",main="Insert size distribution",xlab="Insert size",ylab="Read percent",xaxt="n")
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axis(1,seq(0,1000,100))
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a<-ceiling(weighted.mean(depth[,1],depth[,2])*3/100)*100
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plot(depth[,1],depth[,5],xlim=c(0,a),type="l",col="red",xlab="Base depth",ylab="Cumulative base",main="Base depth cumulative distribution")
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plot(depth[,1],depth[,3],xlim=c(0,a),type="h",col="red",xlab="Base depth",ylab="Base percent",main="Base depth distribution")
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dev.off()
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