caloffset = function(genome){ total_len = sum(as.numeric(genome[,2])) offset = 0 for (i in 1:nrow(genome)) { offset = c(offset,offset[i]+genome[i,2]) } offset } coverage = function(intervals,genome,offset,resolution) { nChr = length(offset) - 1 total_len = offset[nChr+1] nbin = as.integer(total_len / resolution) pos = numeric(0) cov = numeric(0)#coverage col = numeric(0)#color for (i in 1:nChr) { d = x[x[,1]==as.character(genome[i,1]),2:3] d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len) t = table(d) pos = c(pos,as.numeric(row.names(t))) cov = c(cov, as.numeric(t)) col = c(col,numeric(length(t))+i) } list(nbin=nbin,pos=pos,cov=cov,col=col) } # plot coverage # res = genomeView(x,genome,100000) plotcov = function(res,genome,offset,title,uselog) { if (uselog == 'log'){ res$cov = log10(res$cov+1) } ymax = max(res$cov) par(mar=c(5,5,5,1)) plot(res$pos,res$cov,type='h',cex=0.1,cex.axis=2,cex.lab=2,cex.main=3,col=res$col,xaxt='n',main=title,xlab='chromosome',ylab='coverage',frame.plot=F,xlim=c(0,res$nbin),ylim=c(0,ymax)) xticks = numeric(nrow(genome)) for (i in 1:nrow(genome)){ xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)] } mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome))) }