[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:
>> 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.



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

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