[R] Issues getting R to write image files
Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- View this message in context: http://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23977785.html Sent from the R help mailing list archive at Nabble.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] Issues getting R to write image files
Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ 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] Issues getting R to write image files
Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias __ 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] Issues getting R to write image files
Thanks all, I added the dev.off() and although it didn't solve it it no doubt tidies things up on closing. I have got it working now, it is something in the plot() line, as removing all teh options solves it. I will work through adding them in one by one! Kenny Mario Valle wrote: Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ 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. -- View this message in context: http://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23978106.html Sent from the R help mailing list archive at Nabble.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] Issues getting R to write image files
On 11-Jun-09 09:24:42, Tobias Verbeke wrote: Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias I thought of that too -- since the graphics device needs to be closed before writing out to the file is completed and the file is closed. However, it occurred to me that possibly q() would also have that effect, since it closes down R which should have the effect of closing devices, flushing buffers, and closing files (though I do not see this documented under ?q). So I experimented. 1. New R session. 2. Assign values to some variables. 3. Open a tiff() device, plot them, and quit R (no dev.off): tiff(file=temp.tif) plot (X,P, type=l) lines(X,I.b, col=blue ) lines(X,I.m, col=green) lines(X,I.bm^2, col=red) q() 4. End of R session, and temp.tif (which did not exist at the start) contains a good TIFF file with exactly what I expected to see. This confirmed my suspicions. So it sould seem that dev.off() is not the answer. Probably something is wrong along the line of reading in the data, or in specifying what to plot. But I can't see anything obvious in the code, so it may depend on what sort of structure z is, for instance. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 11-Jun-09 Time: 10:43:51 -- XFMail -- __ 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] Issues getting R to write image files
Hi all, Silly missing ) at the end of the plot command! is working now, just need to remove the V1 and V2 that appear under my axis labels! Cheers for all your help guys, much appreciated. Kenny Ted.Harding-2 wrote: On 11-Jun-09 09:24:42, Tobias Verbeke wrote: Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias I thought of that too -- since the graphics device needs to be closed before writing out to the file is completed and the file is closed. However, it occurred to me that possibly q() would also have that effect, since it closes down R which should have the effect of closing devices, flushing buffers, and closing files (though I do not see this documented under ?q). So I experimented. 1. New R session. 2. Assign values to some variables. 3. Open a tiff() device, plot them, and quit R (no dev.off): tiff(file=temp.tif) plot (X,P, type=l) lines(X,I.b, col=blue ) lines(X,I.m, col=green) lines(X,I.bm^2, col=red) q() 4. End of R session, and temp.tif (which did not exist at the start) contains a good TIFF file with exactly what I expected to see. This confirmed my suspicions. So it sould seem that dev.off() is not the answer. Probably something is wrong along the line of reading in the data, or in specifying what to plot. But I can't see anything obvious in the code, so it may depend on what sort of structure z is, for instance. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 11-Jun-09 Time: 10:43:51 -- XFMail -- __ 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. -- View this message in context: http://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23978518.html Sent from the R help mailing list archive at Nabble.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] Issues getting R to write image files
q() does call the internal version of graphics.off() which closes all open graphics devices. On Thu, 11 Jun 2009, Mario Valle wrote: Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ 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.
