a way to show two granges objects on a plot. from http://www.sthda.com/english/wiki/iranges

show_ranges.R

   target.paired.end = GRanges(rep(c(1),each=7), 
                              IRanges(c(7,7,8,9,9,24,25), width=39),
                              strand=rep(c("-"), times=7))
  windows.paired.end = GRanges(rep(c(1),each=3), IRanges(c(7,8,24), width=10), 
                               strand=rep("-", times=3))

   plotir <- function(ir,i, col) { arrows(start(ir)-.5,i,end(ir)+.5,i,code=3,angle=90,lwd=3, col=col) }
  plot(0,0,xlim=c(0,65),ylim=c(0,11),type="n",xlab="",ylab="",xaxt="n")
  axis(1,0:65)
  abline(v=0:65 + .5,col=rgb(0,0,0,.5))
 
  for(i in 1:length(target.paired.end))
      plotir(target.paired.end[i],i, "black")
  for(i in 1:length(windows.paired.end))
    plotir(windows.paired.end[i],i, "red")