R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-linux-gnu (64-bit)

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[Previously saved workspace restored]

> d=read.table("tagCountDistribution.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> d=as.matrix(d)
> d[,2]=d[,2]*100
> 
> if(dim(d)[1]>2){
+ 	pdf(file="tagCountDistribution.pdf")
+ 	barplot(d[2:dim(d)[1],2], main="tag count distribution", xlab="position", ylab="% tags", names.arg=1:(dim(d)[1]-1))
+ 	dev.off()
+ 	}
null device 
          1 
> ## else no plotting because tag count has been set to 1
> 
> d=read.table("tagAutocorrelation.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> d=as.matrix(d)
> #d=d[999:3001,]
> d=d[1501:2501,]
> colnames(d)=c("distance in bp", "same strand", "opposite strand")
> same=cbind(d[,1],d[,2])
> opp=cbind(d[,1],d[,3])
> plot_colors <- c(rgb(r=0.0,g=0.0,b=0.9), "red", "forestgreen",rgb(r=.5,g=0,b=0.5))
> pdf(file="tagAutocorrelation.pdf")
> plot(same, type="l", col=plot_colors[1], ylim=range(d[,2:3]), xlab="Relative distance between reads (bp)", ylab="Total read pairs", cex.lab=0.8, lwd=2)
> lines(opp, type="l", lty=2, lwd=2, col=plot_colors[2])
> legend("bottomright", c("same strand", "opposite strand"), cex=0.8, col=plot_colors, lty=1:2, lwd=2, bty="n")
> dev.off()
null device 
          1 
> 
> d=read.table("tagGCcontent.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> d=as.matrix(d)
> d2p=cbind(d[,1],d[,3])
> g=read.table("genomeGCcontent.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> g=as.matrix(g)
> g2p=cbind(g[,1],g[,3])
> pdf(file="tagGCcontent.pdf")
> plot(d2p, type="l", col=plot_colors[1],  xlab="GC-content of fragments", ylab="Normalized fraction", cex.lab=0.8, lwd=2)
> lines(g2p, type="l", lty=2, lwd=2, col=plot_colors[2])
> legend("topright", c("sample","genome"), cex=0.8, col=plot_colors, lty=1:2, lwd=2, bty="n")
> dev.off()
null device 
          1 
> 
> d=read.table("tagFreqUniq.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> d=as.matrix(d)
> A=cbind(d[,1],d[,2])
> C=cbind(d[,1],d[,3])
> G=cbind(d[,1],d[,4])
> T=cbind(d[,1],d[,5])
> 
> pdf(file="tagFreqUnique.pdf")
> plot(A, type="l", col=plot_colors[1], ylim=range(d[,2:3]),  xlab="Distance from 5'end of reads (bp)", ylab="Nucleotide frequency", cex.lab=0.8, lwd=2)
> lines(C, type="l", lty=2, lwd=2, col=plot_colors[2])
> lines(G, type="l", lty=2, lwd=2, col=plot_colors[3])
> lines(T, type="l", lty=2, lwd=2, col=plot_colors[4])
> legend("bottomright", colnames(d[,2:5]), cex=0.8, col=plot_colors, lty=1:4, lwd=2, bty="n")
> dev.off()
null device 
          1 
> 
> d=read.table("tagFreq.txt", header=TRUE, sep="\t", stringsAsFactors=FALSE)
> d=as.matrix(d)
> A=cbind(d[,1],d[,2])
> C=cbind(d[,1],d[,3])
> G=cbind(d[,1],d[,4])
> T=cbind(d[,1],d[,5])
> 
> pdf(file="tagFreq.pdf")
> plot(A, type="l", col=plot_colors[1], ylim=range(d[,2:3]),  xlab="Distance from 5'end of reads (bp)", ylab="Nucleotide frequency", cex.lab=0.8, lwd=2)
> lines(C, type="l", lty=2, lwd=2, col=plot_colors[2])
> lines(G, type="l", lty=2, lwd=2, col=plot_colors[3])
> lines(T, type="l", lty=2, lwd=2, col=plot_colors[4])
> legend("bottomright", colnames(d[,2:5]), cex=0.8, col=plot_colors, lty=1:4, lwd=2, bty="n")
> dev.off()
null device 
          1 
> 
> proc.time()
   user  system elapsed 
  0.858   0.067   0.948