[O] problems with R graphics

2012-02-29 Thread Matthew Landis
Hello all,

I believe this is my first post on this list, and I'm very new to org-babel, so 
forgive me if I am posting nonsense.  However, I'm really enthused about the 
possibilities org-babel presents.  Unfortunately, I can't seem to get graphics 
to insert themselves properly on export.  I've included an example that 
reproduces my problem below.  For what it's worth, I am using Windows 7 with a 
freshly downloaded issue of Vincent Goulet's package.  Session info:

Emacs version: GNU Emacs 23.4.1 (i386-mingw-nt6.1.7601) of 2012-02-04 on MARVIN
Org mode version 7.8.03
ESS version 5.14
R version 2.14.1

Many thanks for any thoughts or requests for more info.

Matt

org example


#+TITLE: An attempt to make org-mode work with R

In this example, I want to fit a regression and plot it.  I'm
following the examples at the [[http://orgmode.org/worg/org-
contrib/babel/languages/ob-doc-R.html][org manual]] and Erik Iverson's 
[[https://github.com/erikriverson/org-mode-R-tutorial][tutorial]].

* A stand-alone code block

First, create some data, perform a regression, and plot it.  This
works great.
#+begin_src R :results graphics :file regress.png :exports both

  x - runif(n = 100, min = 0, max = 20)
  y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)

  f - lm(y ~ x)

  plot(x, y, bty = 'n')
  abline(f, lty = 'dashed')

#+end_src
Success.

* In code blocks using :session
Now do the same thing, but across an unnamed session

#+begin_src R :session :exports code :results silent

  x - runif(n = 100, min = 0, max = 20)
  y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)

#+end_src

Now, I would like to display the results of the regression as R output.

#+begin_src R :session :results output :exports both
  f - lm(y ~ x)
  summary(f)
#+end_src
Again, success!  This is really going to come in handy.

#+begin_src R :session :results graphics :file regress_session.png :exports both

 plot(x, y, bty = 'n')
 abline(f, lty = 'dashed')

#+end_src
This code block doesn't work. No error, but no file is created.
Also, if I press C-c C-c in the code block, in the org file I get

#+begin_example
#+results:
[[file:regress_session.png]]
#+end_example

But no file is actually created.  What could be going wrong?





Re: [O] problems with R graphics

2012-02-29 Thread Matthew Landis
Matthew Landis landis at isciences.com writes:

 
 Hello all,
...

 Unfortunately, I can't seem to get graphics 
 to insert themselves properly on export.  



 org example
 
...
 * A stand-alone code block
 
 First, create some data, perform a regression, and plot it.  This
 works great.
 #+begin_src R :results graphics :file regress.png :exports both
 
   x - runif(n = 100, min = 0, max = 20)
   y - 5*x^2 + 0.3*x + 3 + rnorm(100, sd = 200)
 
   f - lm(y ~ x)
 
   plot(x, y, bty = 'n')
   abline(f, lty = 'dashed')
 
 #+end_src
 Success.
...

 #+begin_src R :session :results graphics :file regress_session.png :exports 
both
 
  plot(x, y, bty = 'n')
  abline(f, lty = 'dashed')
 
 #+end_src
 This code block doesn't work. No error, but no file is created.

...

I actually figured this one out just now.  If creating a file in a 'stand 
alone' 
code block, the default directory is the directory that the org file itself is 
in.  However, in a 'session' code block, the default directory is something 
else 
(R's default?).  If I specify the full path to the file in the 'session' code 
block, things work better.

Sorry for the noise!

M







Re: [O] problems with R graphics

2012-02-29 Thread Nick Dokos
Matthew Landis lan...@isciences.com wrote:

 Matthew Landis landis at isciences.com writes:
 
 ...
 
  #+begin_src R :session :results graphics :file regress_session.png :exports 
 both
  
   plot(x, y, bty = 'n')
   abline(f, lty = 'dashed')
  
  #+end_src
  This code block doesn't work. No error, but no file is created.
 
 ...
 
 I actually figured this one out just now.  If creating a file in a 'stand 
 alone' 
 code block, the default directory is the directory that the org file itself 
 is 
 in.  However, in a 'session' code block, the default directory is something 
 else 
 (R's default?).  If I specify the full path to the file in the 'session' code 
 block, things work better.
 

Maybe Windows is doing something different, but on Linux, both plots are
produced with no problem, both in the current directory.

Nick