[R] Unwanted white borders on semi-transparent polygons?

[Matthew Neilson]

Hi Brian,

Terribly sorry if I accidentally broke a rule. sessionInfo() produces the following:

> sessionInfo()
R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0 

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "base"     

I cannot upgrade to the latest version of R, since I'm using OS X 10.3.9 (Panther) and the latest builds require 10.4.4 (Tiger) or greater. It's interesting to know that R version 2.4.0 
contains a transparency bug, though - I'll ask IT Services to install the latest version of R on the G5 and see if that helps.

Many thanks for all your help,


-Matt



On Fri Apr 27 12:58 , Prof Brian Ripley <ripley at stats.ox.ac.uk> sent:

>The posting guide says
>
>   For questions about unexpected behavior or a possible bug, you should,
>   at a minimum, copy and paste the output from sessionInfo() into your message.
>
>   If you are using an old version of R and think it does not work
>   properly, upgrade to the latest version and try that, before posting.
>
>[There is a known bug in 2.4.0 related to semi-transparency, fixed in 
>2.4.0.  I would not have attempted to answer a question about 2.1.1, and 
>we do rely on people seeking free technical assistance doing their bit.]
>
>
>On Fri, 27 Apr 2007, Matthew Neilson wrote:
>
>> Thanks for your fast response.
>>
>> I'm using R version 2.1.1 on OS X 10.3.9 to create the pdfs. I have tried viewing the pdf output in both Acrobat 6 and 7 (both display a white border around each polygon) as well 
as
>> Preview (displays fine). I have emailed the pdf file to some correspondents running Windows, and they also see white borders when viewing with Acrobat (version unspecified).
>>
>> I have tried using R version 2.4.0 on a G5 machine (which I can access remotely) running OS X 10.4.8, but the resulting pdf renders incorrectly (i.e. with a white border around 
each
>> polygon) in both Acrobat *and* Preview. So it would appear that the combination of R 2.1.1 and OS X 10.3.9 gives slightly better results - although plots still appear incorrect 
when
>> printed or viewed in Acrobat.
>>
>> Unfortunately, I don't have access to a Windows machine to test this out. Even if I did, many of my scripts include various Unix system calls so I don't think that would be a viable
>> solution. Could this be a bug in the OS X pdf driver?
>
>The R pdf() device is the same on all platforms.
>
>> Many thanks,
>>
>>
>> -Matt
>>
>>
>>
>> On 27 Apr 2007, at 06:42, Prof Brian Ripley wrote:
>>
>>> What version of R, what OS, what version of Acrobat?
>>>
>>> I don't see this in 2.5.0 on Windows (using Acrobat 7: Acrobat does not
>>> exist on Linux, AFAIK).  And reading the PDF produced shows no sign of an
>>> extra object for the border.
>>>
>>> On Fri, 27 Apr 2007, Matthew Neilson wrote:
>>>
>>>> Hey all,
>>>>
>>>> I'm trying to create a plot of two semi-transparent regions. The reason they need to be partially transparent is so that I can see if there's any overlap. Here's some example 
code:
>>>>
>>>> # BEGIN
>>>>
>>>> pdf(file="test.pdf",version="1.4")
>>>> plot(0,0,type="l",ylim=range(-3,3),xlim=range(-1,5))
>>>> polygon(c(0,1,2,3,4,3,2,1,0), c(0,1,2,1,0,-1,-2,-1,0), col=rgb(1,0,0,0.5),
>>>> border=NA)
>>>> polygon(c(1,2,3,4,5,4,3,2,1), c(0,1,2,1,0,-1,-2,-1,0), col=rgb(0,0,1,0.5),
>>>> border=NA)
>>>> dev.off()
>>>>
>>>> # END
>>>>
>>>> The problem with this is that, despite setting "border = NA", I get a
>>>> big white border surrounding each polygon!! Funnily enough, setting the
>>>> alpha channel equal to 1 (as opposed to 0.5) *doesn't* give the border,
>>>> but an alpha channel of 1 produces an opaque polygon! :S
>>>>
>>>> I have read the FAQ, and (unfortunately) turning off line-art smoothing
>>>> does not give the desired effect. Furthermore, my pdfs print with a
>>>> white border surrounding each transparent polygon.
>>>>
>>>> Now, here comes the really bizarre part. Whilst Adobe Acrobat displays
>>>> the unwanted white border, Apple Preview respects the "border=NA"
>>>> argument and shows the two diamonds as they are intended. However,
>>>> opening up the pdf in Illustrator CS reveals that there is in fact a
>>>> transparent (according to Illustrator) border *on top* of each diamond.
>>>> Deleting these two borders (one for each polygon) and re-saving the pdf
>>>> appears to correct the issue. So the obvious question is: how did the
>>>> surrounding borders get there in the first place? A bug in the polygon
>>>> function, perhaps?
>>>>
>>>> Does anyone have any ideas for preventing these unwanted borders around
>>>> semi-transparent polygons (without having to resort to Illustrator)? Has
>>>> anyone else even come across this problem?
>>>>
>>>> Many thanks,
>>>>
>>>>
>>>> -Matt
>>>>
>>>
>>> --
>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>-- 
>Brian D. Ripley,                  ripley at stats.ox.ac.uk
>Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>University of Oxford,             Tel:  +44 1865 272861 (self)
>1 South Parks Road,                     +44 1865 272866 (PA)
>Oxford OX1 3TG, UK                Fax:  +44 1865 272595