Hi All,
I am having trouble outputting ggplot2 graphics to pdf as part of a
script. It works if when I pipe the script into R or if I type the
commands directly into the terminal, but not if I load it using the
source(..) command. In this case the outputted pdf is always size 3611,
and it fails to open with the error "This document contains no pages".
As an example I wrap the create pdf commands around the 1st example in
?ggplot:
$ cat test.R
library(ggplot2)
pdf("test.pdf")
df <- data.frame(
gp = factor(rep(letters[1:3], each = 10)),
y = rnorm(30)
)
ds <- plyr::ddply(df, "gp", plyr::summarise, mean = mean(y), sd =
sd(y))
ggplot(df, aes(gp, y)) +
geom_point() +
geom_point(data = ds, aes(y = mean), colour = 'red', size = 3)
dev.off()
Piping it into R works:
$ R --no-save < test.R
...
$ ll test.pdf
-rw-rw-r-- 1 user group 4842 Mar 2 13:18 test.pdf
This file opens fine and has a graphic. If I repeat the process using
source():
$ R --no-save
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
...
> source("test.R")
>
$ ll test.pdf
-rw-rw-r-- 1 user group 3611 Mar 2 13:25 test.pdf
This file fails to open, and always has the size 3611.
Any help appreciated,
Hugh
This email may have a PROTECTIVE MARKING, for an explanation please see:
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Richard M. Heiberger
2017-Mar-02 13:42 UTC
[R] Problems outputting ggplot2 graphics to pdf
You need the print() statement. See FAQ 7.22 in file
system.file("../../doc/FAQ")
7.22 Why do lattice/trellis graphics not work?
=============================================
The most likely reason is that you forgot to tell R to display the
graph. Lattice functions such as 'xyplot()' create a graph object, but
do not display it (the same is true of *ggplot2*
(https://CRAN.R-project.org/package=ggplot2) graphics, and Trellis
graphics in S-PLUS). The 'print()' method for the graph object produces
the actual display. When you use these functions interactively at the
command line, the result is automatically printed, but in 'source()' or
inside your own functions you will need an explicit 'print()' statement.
On Thu, Mar 2, 2017 at 8:37 AM, Hugh Morgan <h.morgan at har.mrc.ac.uk>
wrote:> Hi All,
>
> I am having trouble outputting ggplot2 graphics to pdf as part of a
> script. It works if when I pipe the script into R or if I type the
> commands directly into the terminal, but not if I load it using the
> source(..) command. In this case the outputted pdf is always size 3611,
> and it fails to open with the error "This document contains no
pages".
>
> As an example I wrap the create pdf commands around the 1st example in
> ?ggplot:
>
> $ cat test.R
>
> library(ggplot2)
>
> pdf("test.pdf")
>
> df <- data.frame(
> gp = factor(rep(letters[1:3], each = 10)),
> y = rnorm(30)
> )
> ds <- plyr::ddply(df, "gp", plyr::summarise, mean = mean(y),
sd = sd(y))
> ggplot(df, aes(gp, y)) +
> geom_point() +
> geom_point(data = ds, aes(y = mean), colour = 'red', size = 3)
>
> dev.off()
>
> Piping it into R works:
>
> $ R --no-save < test.R
>
> ...
>
> $ ll test.pdf
>
> -rw-rw-r-- 1 user group 4842 Mar 2 13:18 test.pdf
>
> This file opens fine and has a graphic. If I repeat the process using
> source():
>
> $ R --no-save
>
> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
> ...
>
>> source("test.R")
>>
>
> $ ll test.pdf
> -rw-rw-r-- 1 user group 3611 Mar 2 13:25 test.pdf
>
> This file fails to open, and always has the size 3611.
>
> Any help appreciated,
>
> Hugh
>
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see:
>
http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>
> ______________________________________________
> 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.
On 02/03/2017 8:37 AM, Hugh Morgan wrote:> Hi All, > > I am having trouble outputting ggplot2 graphics to pdf as part of a > script. It works if when I pipe the script into R or if I type the > commands directly into the terminal, but not if I load it using the > source(..) command. In this case the outputted pdf is always size 3611, > and it fails to open with the error "This document contains no pages". > > As an example I wrap the create pdf commands around the 1st example in > ?ggplot: > > $ cat test.R > > library(ggplot2) > > pdf("test.pdf") > > df <- data.frame( > gp = factor(rep(letters[1:3], each = 10)), > y = rnorm(30) > ) > ds <- plyr::ddply(df, "gp", plyr::summarise, mean = mean(y), sd = sd(y)) > ggplot(df, aes(gp, y)) + > geom_point() + > geom_point(data = ds, aes(y = mean), colour = 'red', size = 3) > > dev.off() > > Piping it into R works: > > $ R --no-save < test.R > > ... > > $ ll test.pdf > > -rw-rw-r-- 1 user group 4842 Mar 2 13:18 test.pdf > > This file opens fine and has a graphic. If I repeat the process using > source(): > > $ R --no-save > > R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch" > ... > > > source("test.R") > > > > $ ll test.pdf > -rw-rw-r-- 1 user group 3611 Mar 2 13:25 test.pdf > > This file fails to open, and always has the size 3611. > > Any help appreciated,ggplot2 graphics only appear when they are printed. By default source("test.R") won't print anything. Set print.eval = TRUE (or echo = TRUE) to get it to print. Duncan Murdoch
Thanks for the help. My test script was changed with: p <- ggplot(df, aes(gp, y)) + geom_point() + geom_point(data = ds, aes(y = mean), colour = 'red', size = 3) print(p) And this now works. Cheers, Hugh On 02/03/17 13:42, Richard M. Heiberger wrote:> You need the print() statement. See FAQ 7.22 in file > system.file("../../doc/FAQ") > > > 7.22 Why do lattice/trellis graphics not work? > =============================================> > The most likely reason is that you forgot to tell R to display the > graph. Lattice functions such as 'xyplot()' create a graph object, but > do not display it (the same is true of *ggplot2* > (https://CRAN.R-project.org/package=ggplot2) graphics, and Trellis > graphics in S-PLUS). The 'print()' method for the graph object produces > the actual display. When you use these functions interactively at the > command line, the result is automatically printed, but in 'source()' or > inside your own functions you will need an explicit 'print()' statement. > > On Thu, Mar 2, 2017 at 8:37 AM, Hugh Morgan <h.morgan at har.mrc.ac.uk> wrote: >> Hi All, >> >> I am having trouble outputting ggplot2 graphics to pdf as part of a >> script. It works if when I pipe the script into R or if I type the >> commands directly into the terminal, but not if I load it using the >> source(..) command. In this case the outputted pdf is always size 3611, >> and it fails to open with the error "This document contains no pages". >> >> As an example I wrap the create pdf commands around the 1st example in >> ?ggplot: >> >> $ cat test.R >> >> library(ggplot2) >> >> pdf("test.pdf") >> >> df <- data.frame( >> gp = factor(rep(letters[1:3], each = 10)), >> y = rnorm(30) >> ) >> ds <- plyr::ddply(df, "gp", plyr::summarise, mean = mean(y), sd = sd(y)) >> ggplot(df, aes(gp, y)) + >> geom_point() + >> geom_point(data = ds, aes(y = mean), colour = 'red', size = 3) >> >> dev.off() >> >> Piping it into R works: >> >> $ R --no-save < test.R >> >> ... >> >> $ ll test.pdf >> >> -rw-rw-r-- 1 user group 4842 Mar 2 13:18 test.pdf >> >> This file opens fine and has a graphic. If I repeat the process using >> source(): >> >> $ R --no-save >> >> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch" >> ... >> >>> source("test.R") >>> >> $ ll test.pdf >> -rw-rw-r-- 1 user group 3611 Mar 2 13:25 test.pdf >> >> This file fails to open, and always has the size 3611. >> >> Any help appreciated, >> >> Hugh >> >> >> >> This email may have a PROTECTIVE MARKING, for an explanation please see: >> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm >> >> ______________________________________________ >> 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.This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm