[R] blank pdf output when called in a loop
Hi,
I'm hitting a strange problem where pdf plots that I'm trying to make
are blank, only when produced from within a loop. The pdf contains 0 page.
I've narrowed the problem to this minimal script that invariably
produces an empty pdf with my setup:
pdf(/local/scratch/1.pdf, width=8, height=8)
for (k in 1) {
wireframe(volcano)
}
dev.off()
The odd thing is that
pdf(/local/scratch/1.pdf, width=8, height=8)
wireframe(volcano)
dev.off()
works fine!
Am I doing something wrong here? I've tried on two different systems,
Linux or Mac.
Thanks,
Nico
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
[6] LC_MESSAGES=en_US.UTF-8LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.18-5 custom_1.1
loaded via a namespace (and not attached):
[1] grid_2.11.0
--
Nicolas STRANSKY, Ph.D.
Computational Biologist, Cancer Program
Broad Institute of MIT and Harvard
5CC-1339 | 7 Cambridge Center | Cambridge, MA 02142, USA
Phone: +1 617 714 7564 |n...@broadinstitute.org
__
R-help@r-project.org 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.
Re: [R] blank pdf output when called in a loop
Hi Nicolas,
You nee to explicitly wrap it in print() when it is inside a loop (if
I'm not mistaken also when inside a function). With lattice loaded,
you can find the specific print methods by methods(print) . From your
example:
pdf(temp1.pdf, width=8, height=8)
for(k in 1) {
print(wireframe(volcano))
}
dev.off()
HTH,
Josh
On Tue, Jul 20, 2010 at 4:02 PM, Nicolas STRANSKY
stran...@broadinstitute.org wrote:
Hi,
I'm hitting a strange problem where pdf plots that I'm trying to make
are blank, only when produced from within a loop. The pdf contains 0 page.
I've narrowed the problem to this minimal script that invariably
produces an empty pdf with my setup:
pdf(/local/scratch/1.pdf, width=8, height=8)
for (k in 1) {
wireframe(volcano)
}
dev.off()
The odd thing is that
pdf(/local/scratch/1.pdf, width=8, height=8)
wireframe(volcano)
dev.off()
works fine!
Am I doing something wrong here? I've tried on two different systems,
Linux or Mac.
Thanks,
Nico
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.18-5 custom_1.1
loaded via a namespace (and not attached):
[1] grid_2.11.0
--
Nicolas STRANSKY, Ph.D.
Computational Biologist, Cancer Program
Broad Institute of MIT and Harvard
5CC-1339 | 7 Cambridge Center | Cambridge, MA 02142, USA
Phone: +1 617 714 7564 | n...@broadinstitute.org
__
R-help@r-project.org 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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org 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.
Re: [R] blank pdf output when called in a loop
On Jul 20, 2010, at 7:21 PM, Joshua Wiley wrote:
Hi Nicolas,
You nee to explicitly wrap it in print() when it is inside a loop (if
I'm not mistaken also when inside a function). With lattice loaded,
you can find the specific print methods by methods(print) .
The interpreter handles finding the proper print methods. You just
need to have a clear list in your mind regarding what is base graphics
(e.g.plot) and what is grid graphics (e.g. xyplot and qplot). This is
part of the FAQ which points out that this also applies to any
source()-ed code:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
(which points out that this applies to ggplot2 functions as well.)
To further confuse the issue, not all functions named plot are
dispatched to base graphics. Some are dispatched to lattice graphics.
--
David.
From your
example:
pdf(temp1.pdf, width=8, height=8)
for(k in 1) {
print(wireframe(volcano))
}
dev.off()
HTH,
Josh
On Tue, Jul 20, 2010 at 4:02 PM, Nicolas STRANSKY
stran...@broadinstitute.org wrote:
Hi,
I'm hitting a strange problem where pdf plots that I'm trying to make
are blank, only when produced from within a loop. The pdf contains
0 page.
I've narrowed the problem to this minimal script that invariably
produces an empty pdf with my setup:
pdf(/local/scratch/1.pdf, width=8, height=8)
for (k in 1) {
wireframe(volcano)
}
dev.off()
The odd thing is that
pdf(/local/scratch/1.pdf, width=8, height=8)
wireframe(volcano)
dev.off()
works fine!
Am I doing something wrong here? I've tried on two different systems,
Linux or Mac.
Thanks,
Nico
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
[6] LC_MESSAGES=en_US.UTF-8LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.18-5 custom_1.1
loaded via a namespace (and not attached):
[1] grid_2.11.0
--
Nicolas STRANSKY, Ph.D.
Computational Biologist, Cancer Program
Broad Institute of MIT and Harvard
5CC-1339 | 7 Cambridge Center | Cambridge, MA 02142, USA
Phone: +1 617 714 7564 |n...@broadinstitute.org
__
R-help@r-project.org 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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org 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.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org 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.
Re: [R] blank pdf output when called in a loop
On 7/20/10 8:14 PM, David Winsemius wrote: On Jul 20, 2010, at 7:21 PM, Joshua Wiley wrote: Hi Nicolas, You nee to explicitly wrap it in print() when it is inside a loop (if I'm not mistaken also when inside a function). With lattice loaded, you can find the specific print methods by methods(print) . The interpreter handles finding the proper print methods. You just need to have a clear list in your mind regarding what is base graphics (e.g.plot) and what is grid graphics (e.g. xyplot and qplot). This is part of the FAQ which points out that this also applies to any source()-ed code: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f Thanks! print() indeed does the job. I was fighting with this for quite some time, it didn't occur to me to use print(). Nico -- Nicolas STRANSKY, Ph.D. Computational Biologist, Cancer Program Broad Institute of MIT and Harvard 5CC-1339 | 7 Cambridge Center | Cambridge, MA 02142, USA Phone: +1 617 714 7564 |n...@broadinstitute.org __ R-help@r-project.org 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.
