R help - Apr 2007 - Unwanted white borders on semi-transparent polygons?

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

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

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?

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

Hi Roger,

Yes, that's the FAQ to which I was referring in my original email.
Unfortunately, turning off smoothing for line art (as suggested in the FAQ) did
not work for me.

Many thanks,


-Matt



On Fri Apr 27 12:32 , Roger Bivand <Roger.Bivand at nhh.no> sent:
>Matt:
>
>Is this by any chance a version of FAQ 7.36, which turned out to be the 
>smooth line art flag in Adobe Reader?
>
>Roger
>
>
>
>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?
>> 
>> 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.
>> 
>
>-- 
>Roger Bivand
>Economic Geography Section, Department of Economics, Norwegian School of
>Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>e-mail: Roger.Bivand at nhh.no
>

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