When creating more complex scatter plots (especially when building multiple plots on the same set of axes using par(new=T)), I often set the ylim myself to some custom value; however, you will find that even in these cases base plot in R will add a “buffer” to the upper and lower limits of your y-axes. I’ve always wondered just EXACTLY what this buffer was, and after a little bit of searching, I found this very informative (and useful–due to the nifty yaxs=’i’ trick) post. Anyhow, the answer, it seems, is 4%.