[R] Unwanted white borders on semi-transparent polygons?
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Apr 27 19:43:34 CEST 2007
On Fri, 27 Apr 2007, Matthew Neilson wrote:
> Hey again,
>
> Just to let you know that I managed to test out R-2.5.0, and the transparency
> glitch has thankfully disappeared. I apologise for wasting your time with
> this.
>
> One final question, though. Did you mean to say that the known transparency
> bug was fixed in version 2.5.0? Or was it fixed in a patched version of
> R-2.4.0? Only asking because, if the final Panther binary (version 2.4.0)
> available on CRAN doesn't fix the bug, there's no point in me installing this
> on top of my happily working (and otherwise fully functional) version of R.
I meant to say '2.4.0 patched', which became 2.4.1. The release of 2.4.0
has the bug: NEWS says
o A request for an opaque colour in the pdf() device after a
translucent one did not set the transparency back to opaque in
2.4.0.
Semi-transparent background colours were not being plotted on
the pdf() device.
>
> Many thanks,
>
>
> -Matt
>
>
>
> On 27 Apr 2007, at 13:35, Matthew Neilson wrote:
>
>> 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
>>>>
>>>> ______________________________________________
>>>> R-help at stat.math.ethz.ch 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.
>>>>
>>>
>>> --
>>> 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
>>
>> ______________________________________________
>> R-help at stat.math.ethz.ch 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.
>>
>>
>
> --
> ************************************
> Matthew Neilson
> University of Strathclyde
> Department of Mathematics
> Livingstone Tower
> 26 Richmond Street
> Glasgow G1 1XH
>
> Tel : + 44(0)141 548 4559
> e-mail : rs.mnei at maths.strath.ac.uk
> ************************************
>
--
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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