I am using plot() for over 1 mln data points and it turns out to be very slow.
Is there any way to improve the speed including programming and hardware
have you looked at the tabplot package. it is designed specifically for large data http://cran.r-project.org/web/packages/tabplot/ I use that its faster than using hexbin (or even the default sunflower plots for overplotting)
also i think Hadley wrote something on DS 's blog modifying ggplot for big data at http://blog.revolutionanalytics.com/2011/10/ggplot2-for-big-data.html
"""I'm currently with working another student, Yue Hu, to turn our research into a robust R package.""" October 21, 2011
Maybe we can ask Hadley if the updated ggplot3 is ready