Re: [R] Scatterplot Showing All Points

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Tue, 18 Dec 2007 10:58:09 -0500

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_at_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. Received on Tue 18 Dec 2007 - 16:01:52 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 18 Dec 2007 - 17:30:19 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.