[BioC] save R graphics device output in a file

[Sean Davis]

On Mon, Apr 14, 2008 at 4:01 PM, carol white <wht_crl at yahoo.com> wrote:
> Thanks for your reply.
>
>  I wrote  a script, namely my_script and run it as
>  R < my_script > res --no-save &
>
>  my_script contains:
>
>  library (geneplotter)
>  library (grDevices)
>  hist (mat) # mat is a matrix
>  savepng ("Rtmp", ".")
>  dev.off()
>  q("no")

Try:
png('stuff.png')
hist(mat)
dev.off()


>  ***********************************3
>  so Rtmp.png is created at the end but with 0 byte and res (output file) contains:
>  > library (geneplotter)
>  > library (grDevices)
>  > hist (mat)
>  > savepng ("Rtmp", ".")
>  [1] "./Rtmp.png"
>  > dev.off()
>  null device
>           1
>  > q("no")
>
>
>  but when running in R:
>  *****************************
>  library (geneplotter)
>  Loading required package: annotate
>  Loading required package: Biobase
>  Loading required package: tools
>
>  Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>  Loading required package: lattice
>  KernSmooth 2.22 installed
>  Copyright M. P. Wand 1997
>  > library (grDevices)
>  > hist (mat)
>  > savepng ("Rtmp", ".")
>  [1] "./Rtmp.png"
>  > dev.off()
>  null device
>           1
>  > q("no")
>
>  ./Rtmp.png is created correctly (a non-zero byte image)
>
>  I use R 2.5.1
>
>  thanks
>
>  Florian Hahne <fhahne at fhcrc.org> wrote: Hi Carol,
>  In order to save graphics on a file device you need to properly close
>  this device after the plotting, that is, use dev.off() I am not sure
>  what you mean by "running R in the background". Did you start it via R
>  CMD batch or something similar as a background process? In any case,
>  the proper use of jpeg() and dev.off() should create a valid image
>  file irespective of that, unless you are on remote machine without x11
>  port forwarding, which again should result in a number of errors.
>  Sending a brief example of code that illustrates your problem and at
>  least some information about your R version would also help
>  Cheers
>  Florian
>
>
>
>  On 14.04.2008, at 08:22, carol white  wrote:
>
>  > Hi,
>  > I tried to use savepng (library geneplotter) or jpeg (grDevices) to
>  > save the R output image in a file. When I run R in foreground,
>  > savepng saves the image in a file but when I run R in background (in
>  > a unix terminal shell), a file is created but with 0 byte. When the
>  > jpeg is used in R in bg or fg, a file is created with 0 byte. Why is
>  > the image not saved when I run the R in bg?
>  >
>  > Regards,
>  >
>  > carol
>  >
>  >
>  >
>  >
>  >
>  > ____________________________________________________________________________________
>
>
>  > Be a better friend, newshound, and
>  >
>  >    [[alternative HTML version deleted]]
>  >
>  > _______________________________________________
>  > Bioconductor mailing list
>  > Bioconductor at stat.math.ethz.ch
>  > https://stat.ethz.ch/mailman/listinfo/bioconductor
>  > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>         [[alternative HTML version deleted]]
>
>  _______________________________________________
>  Bioconductor mailing list
>  Bioconductor at stat.math.ethz.ch
>  https://stat.ethz.ch/mailman/listinfo/bioconductor
>  Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>