Scatterplot Showing All Points
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