R help - Mar 2019 - [FORGED] R cairo_pdf function does not respect plotting boundaries

Hello all,

When producing a plot in R using the cairo_pdf device, the resultant plot does
not respect the plotting boundaries. Lines and shaded regions will spill over
the lower x-axis and the right-side y-axis (sides 1 and 4). I would like to know
if it is possible to fix this behaviour when using 'cairo_pdf' in R?

As an example, see the image at this web link:
https://i.stack.imgur.com/0lfZd.png

This image is a screenshot of a PDF file constructed using the following minimum
working example code:

cairo_pdf(file="test.pdf", width=0.5, height=0.5)
par("mar"=c(0.25,0.25,0.25,0.25))
plot(NA, xlim=c(0,1), ylim=c(0,1), axes=FALSE)
polygon(x=c(-1,-1,2,2), y=c(-1,2,2,-1), density=5, col="green3",
lwd=10)
abline(h=0.25, col="red", lwd=5)
abline(h=0.75, col="hotpink", lwd=5, lend=1)
abline(v=0.25, col="blue", lwd=5)
abline(v=0.75, col="cyan", lwd=5, lend=1)
box()
dev.off()

Here I'm plotting a shaded region in green using 'polygon', with
boundaries that lie outside the plot. I'm also drawing two sets of
horizontal/vertical lines using 'abline'. The first in each pair uses
standard rounded line caps, whilst the second in each pair uses butt line caps.

As you can see, the shading lines and the default rounded-end ablines all extend
beyond the plotting region along the lower and right-hand side axes. Only when
using 'lend=1' am I able to contain the ablines to the plotting region.
I know of no such fix for the shading lines however.

I would naively expect the R plotting region to be respected, and for it to be
impossible to plot outside of this region unless explicitly specified by the
user.

I have tested this on the other cairo devices (SVG and PS), and also reproduce
the same behaviour, indicating that this is an issue with the cairo graphics
API, or its implementation within R.

This behaviour does not occur when using the standard R 'pdf' graphics
device. I would switch to 'pdf' in general, however, 'cairo_pdf'
has several advantages over 'pdf', notably, reduced output file sizes on
occasion and support for a larger array of UTF-8 characters, so ideally I would
prefer to use cairo_pdf.

I should note that I have also posted this message on StackOverflow at this web
link:
https://stackoverflow.com/questions/54892809/r-cairo-pdf-function-does-not-respect-plotting-boundaries

Thank you in advance for any insights into this issue.

Sincerely,
Lee Kelvin



--
Dr Lee Kelvin
Department of Physics
UC Davis
One Shields Avenue
Davis, CA 95616
USA

Ph: +1 (530) 752-1500
Fax: +1 (530) 752-4717


	[[alternative HTML version deleted]]

Hi

(cc'ed to r-devel where further discussion should probably take place)

Thanks Lee.  I see that problem.

There is a "+ 1" in the Cairo device code for setting the clipping
region
(https://github.com/wch/r-source/blob/ba600867f2a94e46cf9eb75dc8b37f12b08a4561/src/library/grDevices/src/cairo/cairoFns.c#L156)


Remove the "+ 1" and the problem goes away (for your example at
least).

The comment on the line above that code suggests that the "+ 1" was 
modelled on the X11 device code, but X11 deals in integer pixels and 
Cairo (at the API level) does not, so it would seem that the "+ 1" is 
just unnecessary.

However, I have a slight nagging worry that we have been here before, so 
I would like to do some more testing before committing that change.

Paul

On 1/03/19 8:13 AM, Lee Steven Kelvin wrote:
> Hello all,
> 
> When producing a plot in R using the cairo_pdf device, the resultant plot
does not respect the plotting boundaries. Lines and shaded regions will spill
over the lower x-axis and the right-side y-axis (sides 1 and 4). I would like to
know if it is possible to fix this behaviour when using 'cairo_pdf' in
R?
> 
> As an example, see the image at this web link:
https://i.stack.imgur.com/0lfZd.png
> 
> This image is a screenshot of a PDF file constructed using the following
minimum working example code:
> 
> cairo_pdf(file="test.pdf", width=0.5, height=0.5)
> par("mar"=c(0.25,0.25,0.25,0.25))
> plot(NA, xlim=c(0,1), ylim=c(0,1), axes=FALSE)
> polygon(x=c(-1,-1,2,2), y=c(-1,2,2,-1), density=5, col="green3",
lwd=10)
> abline(h=0.25, col="red", lwd=5)
> abline(h=0.75, col="hotpink", lwd=5, lend=1)
> abline(v=0.25, col="blue", lwd=5)
> abline(v=0.75, col="cyan", lwd=5, lend=1)
> box()
> dev.off()
> 
> Here I'm plotting a shaded region in green using 'polygon',
with boundaries that lie outside the plot. I'm also drawing two sets of
horizontal/vertical lines using 'abline'. The first in each pair uses
standard rounded line caps, whilst the second in each pair uses butt line caps.
> 
> As you can see, the shading lines and the default rounded-end ablines all
extend beyond the plotting region along the lower and right-hand side axes. Only
when using 'lend=1' am I able to contain the ablines to the plotting
region. I know of no such fix for the shading lines however.
> 
> I would naively expect the R plotting region to be respected, and for it to
be impossible to plot outside of this region unless explicitly specified by the
user.
> 
> I have tested this on the other cairo devices (SVG and PS), and also
reproduce the same behaviour, indicating that this is an issue with the cairo
graphics API, or its implementation within R.
> 
> This behaviour does not occur when using the standard R 'pdf'
graphics device. I would switch to 'pdf' in general, however,
'cairo_pdf' has several advantages over 'pdf', notably, reduced
output file sizes on occasion and support for a larger array of UTF-8
characters, so ideally I would prefer to use cairo_pdf.
> 
> I should note that I have also posted this message on StackOverflow at this
web link:
https://stackoverflow.com/questions/54892809/r-cairo-pdf-function-does-not-respect-plotting-boundaries
> 
> Thank you in advance for any insights into this issue.
> 
> Sincerely,
> Lee Kelvin
> 
> 
> 
> --
> Dr Lee Kelvin
> Department of Physics
> UC Davis
> One Shields Avenue
> Davis, CA 95616
> USA
> 
> Ph: +1 (530) 752-1500
> Fax: +1 (530) 752-4717
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
> 
-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/

Hi Paul,

Great, thank you for looking in to this, and I'm glad that you're able
to reproduce it at your end too.

From your reply, I'm happy that it seems like the fix may be fairly trivial,
but I understand the necessity for caution.

If there's anything else I can do to help, please do let me know.

Thank you again,
Best,
Lee


On Monday, 4 March 2019, Paul Murrell <paul at
stat.auckland.ac.nz<mailto:paul at stat.auckland.ac.nz>> wrote:
Hi

(cc'ed to r-devel where further discussion should probably take place)

Thanks Lee.  I see that problem.

There is a "+ 1" in the Cairo device code for setting the clipping
region
(https://github.com/wch/r-source/blob/ba600867f2a94e46cf9eb75dc8b37f12b08a4561/src/library/grDevices/src/cairo/cairoFns.c#L156)

Remove the "+ 1" and the problem goes away (for your example at
least).

The comment on the line above that code suggests that the "+ 1" was
modelled on the X11 device code, but X11 deals in integer pixels and Cairo (at
the API level) does not, so it would seem that the "+ 1" is just
unnecessary.

However, I have a slight nagging worry that we have been here before, so I would
like to do some more testing before committing that change.

Paul

On 1/03/19 8:13 AM, Lee Steven Kelvin wrote:
Hello all,

When producing a plot in R using the cairo_pdf device, the resultant plot does
not respect the plotting boundaries. Lines and shaded regions will spill over
the lower x-axis and the right-side y-axis (sides 1 and 4). I would like to know
if it is possible to fix this behaviour when using 'cairo_pdf' in R?

As an example, see the image at this web link:
https://i.stack.imgur.com/0lfZd.png

This image is a screenshot of a PDF file constructed using the following minimum
working example code:

cairo_pdf(file="test.pdf", width=0.5, height=0.5)
par("mar"=c(0.25,0.25,0.25,0.25))
plot(NA, xlim=c(0,1), ylim=c(0,1), axes=FALSE)
polygon(x=c(-1,-1,2,2), y=c(-1,2,2,-1), density=5, col="green3",
lwd=10)
abline(h=0.25, col="red", lwd=5)
abline(h=0.75, col="hotpink", lwd=5, lend=1)
abline(v=0.25, col="blue", lwd=5)
abline(v=0.75, col="cyan", lwd=5, lend=1)
box()
dev.off()

Here I'm plotting a shaded region in green using 'polygon', with
boundaries that lie outside the plot. I'm also drawing two sets of
horizontal/vertical lines using 'abline'. The first in each pair uses
standard rounded line caps, whilst the second in each pair uses butt line caps.

As you can see, the shading lines and the default rounded-end ablines all extend
beyond the plotting region along the lower and right-hand side axes. Only when
using 'lend=1' am I able to contain the ablines to the plotting region.
I know of no such fix for the shading lines however.

I would naively expect the R plotting region to be respected, and for it to be
impossible to plot outside of this region unless explicitly specified by the
user.

I have tested this on the other cairo devices (SVG and PS), and also reproduce
the same behaviour, indicating that this is an issue with the cairo graphics
API, or its implementation within R.

This behaviour does not occur when using the standard R 'pdf' graphics
device. I would switch to 'pdf' in general, however, 'cairo_pdf'
has several advantages over 'pdf', notably, reduced output file sizes on
occasion and support for a larger array of UTF-8 characters, so ideally I would
prefer to use cairo_pdf.

I should note that I have also posted this message on StackOverflow at this web
link:
https://stackoverflow.com/questions/54892809/r-cairo-pdf-function-does-not-respect-plotting-boundaries

Thank you in advance for any insights into this issue.

Sincerely,
Lee Kelvin



--
Dr Lee Kelvin
Department of Physics
UC Davis
One Shields Avenue
Davis, CA 95616
USA

Ph: +1 (530) 752-1500
Fax: +1 (530) 752-4717


        [[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To
UNSUBSCRIBE and more, see
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.


--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz<mailto:paul at stat.auckland.ac.nz>
http://www.stat.auckland.ac.nz/~paul/


--
Dr Lee Kelvin
Department of Physics
UC Davis
One Shields Avenue
Davis, CA 95616
USA

Ph: +1 (530) 752-1500
Fax: +1 (530) 752-4717


	[[alternative HTML version deleted]]