[R] Scatterplot Showing All Points
James W. MacDonald
jmacdon at med.umich.edu
Tue Dec 18 16:02:00 CET 2007
Duncan Murdoch wrote:
> On 18/12/2007 7:31 AM, Antony Unwin wrote:
>> 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
>> (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
> 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)
> 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(jitter(x), jitter(y))
Another alternative is smoothscatter() in the geneplotter package from
Bioconductor, which does a pretty reasonable job with these example data.
> makes the distribution quite clear.
> I wouldn't use the default pch if I had 50000 points, but with pch=".",
> it's not so bad even in that case.
> Duncan Murdoch
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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