create qq plot where you can specify the upper limit on the y-axis.

qq-with-ymax.r

qq = function(pvector, ymax=NA, ...) {
  if (!is.numeric(pvector)) stop("D'oh! P value vector is not numeric.")
  pvector <- pvector[!is.na(pvector) & pvector<1 & pvector>0]
  o = -log10(sort(pvector,decreasing=F))
  e = -log10( ppoints(length(pvector) ))
  if (!is.numeric(ymax) | ymax<max(o)) ymax <- max(o)
  plot(e,o,pch=19,cex=1, xlab=expression(Expected~~-log[10](italic(p))), ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,ymax), ...)
  abline(0,1,col="red")
}

# automatically set ymax
qq(runif(1000))

# if you specify a ymax that's below what it should have been, it will still automatically scale
qq(runif(1000), ymax=1)

# if you specify ymax above max observed -logp, the y axis will expand
qq(runif(1000), ymax=10)