[O] R plots always exported to Rplots.pdf
Hi, I'm trying to generate a report with R plots using org-mode but no matter what header arguments are you the generated files are always called Rplots.pdf This is what my code block looks like: #+NAME: pvals_waw #+BEGIN_SRC R :file fig1.png :exports results pvals = read.table(waw_data.txt, header=T) plot(pvals$pvalue, pvals$length) #+END_SRC after evaluating the code block I get #+RESULTS: pvals_waw [[file:fig1.png]] but I can see that the plot is in Rplots.pdf so subsequent attempt to export Latex/PDF fail. I'm using org 20130522 and R 3.0. Best, Greg -- Greg Slodkowicz PhD student, Nick Goldman group EMBL-EBI
Re: [O] R plots always exported to Rplots.pdf
Hi Greg, On Wed, May 22, 2013 at 8:23 AM, Greg Slodkowicz gr...@ebi.ac.uk wrote: [snip] This is what my code block looks like: #+NAME: pvals_waw #+BEGIN_SRC R :file fig1.png :exports results pvals = read.table(waw_data.txt, header=T) plot(pvals$pvalue, pvals$length) #+END_SRC Have you tried (something like) this? #+BEGIN_SRC R :exports results :results graphics :file fig1.png I hope this helps, -- Jay
Re: [O] R plots always exported to Rplots.pdf
That solves it, many thanks! - Greg On Wed, May 22, 2013 at 2:38 PM, Jay Kerns gjkerns...@gmail.com wrote: Hi Greg, On Wed, May 22, 2013 at 8:23 AM, Greg Slodkowicz gr...@ebi.ac.uk wrote: [snip] This is what my code block looks like: #+NAME: pvals_waw #+BEGIN_SRC R :file fig1.png :exports results pvals = read.table(waw_data.txt, header=T) plot(pvals$pvalue, pvals$length) #+END_SRC Have you tried (something like) this? #+BEGIN_SRC R :exports results :results graphics :file fig1.png I hope this helps, -- Jay -- Greg Slodkowicz PhD student, Nick Goldman group EMBL-EBI
Re: [O] R plots always exported to Rplots.pdf
Greg Slodkowicz gr...@ebi.ac.uk writes: Hi, I'm trying to generate a report with R plots using org-mode but no matter what header arguments are you the generated files are always called Rplots.pdf This is what my code block looks like: #+NAME: pvals_waw #+BEGIN_SRC R :file fig1.png :exports results pvals = read.table(waw_data.txt, header=T) plot(pvals$pvalue, pvals$length) #+END_SRC after evaluating the code block I get #+RESULTS: pvals_waw [[file:fig1.png]] but I can see that the plot is in Rplots.pdf so subsequent attempt to export Latex/PDF fail. I'm using org 20130522 and R 3.0. Best, Greg The following example demonstrates the combination of header arguments required to generate the correctly named output. #+name: input | 1 | 2 | | 2 | 4 | | 3 | 9 | #+NAME: pvals_waw #+headers: :var input=input #+BEGIN_SRC R :results graphics :file output.pdf plot(input) #+END_SRC after evaluating the code block I get #+RESULTS: pvals_waw [[file:output.pdf]] This should be documented on Worg, but there is no doubt that there is still work to be done on language-specific header argument documentation. -- Eric Schulte http://cs.unm.edu/~eschulte
