[R] Scatterplot Showing All Points

[Duncan Murdoch]

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