R plots always exported to Rplots.pdf

R plots always exported to Rplots.pdf

[Greg Slodkowicz]

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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

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Re: R plots always exported to Rplots.pdf

[Eric Schulte]

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Greg Slodkowicz <gregs@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.


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#+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]]

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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

Re: R plots always exported to Rplots.pdf

[Jay Kerns]

Hi Greg,

On Wed, May 22, 2013 at 8:23 AM, Greg Slodkowicz <gregs@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: R plots always exported to Rplots.pdf

[Greg Slodkowicz]

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That solves it, many thanks!

- Greg


On Wed, May 22, 2013 at 2:38 PM, Jay Kerns <gjkernsysu@gmail.com> wrote:

> Hi Greg,
>
> On Wed, May 22, 2013 at 8:23 AM, Greg Slodkowicz <gregs@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

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