On 18/12/2007 10:02 AM, James W. MacDonald wrote: > Duncan Murdoch wrote: >> On 18/12/2007 7:31 AM, Antony Unwin wrote: >>> Wayne, >>> >>> Try the iplot command in iPlots. You can then vary both the >>> pointsize and the transparency of your scatterplot interactively and >>> decide which scatterplot conveys the information best. Sometimes >>> it's helpful to use more than one scatterplot when presenting your >>> results. >>> >>> (I must admit to being very surprised that jittering and sunflower >>> plots have been suggested for a dataset of 5000 points. Do those who >>> mentioned these methods have examples on that scale where they are >>> effective?) >> Sure. The original post said there were about 50-60 unique locations. >> This plot: >> >> x <- rbinom(5000, 20, 0.15) >> y <- rbinom(5000, 20, 0.15) >> plot(x,y) >> >> has a few more unique locations; tune those probabilities if you want it >> closer. Due to the overlap, the distribution is very unclear. But this >> plot >> >> plot(jitter(x), jitter(y)) > > Another alternative is smoothscatter() in the geneplotter package from > Bioconductor, which does a pretty reasonable job with these example data.
Yes, I agree. (As an aside, there's actually a capital S in smoothScatter(), and it's a bit of a pain to install, because geneplotter depends on something that depends on DBI, which is not so easily available these days.) Duncan Murdoch ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
