[R] 3D-scatterplots - high quality rendering?

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Fri Oct 22 12:43:39 CEST 2010

Quoting Duncan Murdoch <murdoch.duncan at gmail.com>:

> On 21/10/2010 1:23 PM, J.delasHeras at ed.ac.uk wrote:
>> Quoting Duncan Murdoch<murdoch.duncan at gmail.com>:
>>>  J.delasHeras at ed.ac.uk wrote:
>>>>  I have just started using the package 'rgl' to explore my data as a
>>>>   3D scatterplot.
>>>>  It's a great tool. But I would like to be able to save some graph
>>>>  views and it appears the only format available is 'png' and it
>>>>  doesn't look that nice. It is excellent to work with on screen and
>>>>   explore/play, but when it comes to producing a good quality
>>>>  graphic   I'm a bit disappointed.
>>>>  So the questions I have are:
>>>>  1) is there a way to render the graph in the RGL device as a high
>>>>  quality graphic?
>>>  You can use rgl.postscript for various other formats, but you may find
>>>  the bitmap output is better.  In particular, shading is not always done
>>>  correctly.
>>>  Duncan Murdoch
>> Hi Duncan,
>> thanks for that.
>> Stupidly I hadn't realised only part of the manual had printed so I
>> was missing a lot of interesting options, not only this one but others
>> to animate views.
>> The type of plots I'm producing are similar to these:
>> library(rgl)
>> m<-matrix(rnorm(900),ncol=3)
>> plot3d(m,col=rainbow(6),type="s",size=0.8)
>> I tried rgl.postscript to save to pdf, as it's become my default
>> format when I want smooth plots using standard R graphics X11()
>> It looks smoother, but I get some "artifacts" in that the edges and
>> colouring of a number of spheres are rough, or incompletely coloured
>> (imagine a small scratch on a photograph)
>> using 'rgl.snapshot' to output a bitmap (png) with small spheres it
>> doesn't look that great. The default squares look fine 'though.
> The way I usually save output is to use rgl.snapshot after increasing
> the size of the window as large as possible.  At 1000 x 1000 pixels I
> find the output okay.
> How large is possible will depend on your hardware and OpenGL driver.
> Usually you can't make it any bigger than your physical monitor, and
> you can't always make it that big.
> Duncan Murdoch

It's working pretty nicely for me, enlarging the window like you say.
I have an interesting looking set of data that I was able to explore  
very easily using different thresholds/colour codes and I just made a  
pretty cool figure. Surprisingly easy once I had the whole manual  
printed in front of me and with your comments.

Again, many thanks for your help and your work in the 'rgl' package!



Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507095
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