Re: [R] Scatterplot Showing All Points

From: James W. MacDonald <jmacdon_at_med.umich.edu>
Date: Tue, 18 Dec 2007 10:02:00 -0500

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.

Best,

Jim

>
> 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
> 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.

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

______________________________________________
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 - 15:05:49 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 - 16:30:19 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.