* problems with R graphics
@ 2012-03-01 2:18 Matthew Landis
2012-03-01 2:47 ` Matthew Landis
0 siblings, 1 reply; 3+ messages in thread
From: Matthew Landis @ 2012-03-01 2:18 UTC (permalink / raw)
To: emacs-orgmode
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?
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: problems with R graphics
2012-03-01 2:18 problems with R graphics Matthew Landis
@ 2012-03-01 2:47 ` Matthew Landis
2012-03-01 5:45 ` Nick Dokos
0 siblings, 1 reply; 3+ messages in thread
From: Matthew Landis @ 2012-03-01 2:47 UTC (permalink / raw)
To: emacs-orgmode
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
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: problems with R graphics
2012-03-01 2:47 ` Matthew Landis
@ 2012-03-01 5:45 ` Nick Dokos
0 siblings, 0 replies; 3+ messages in thread
From: Nick Dokos @ 2012-03-01 5:45 UTC (permalink / raw)
To: Matthew Landis; +Cc: nicholas.dokos, emacs-orgmode
Matthew Landis <landis@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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2012-03-01 2:18 problems with R graphics Matthew Landis
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2012-03-01 5:45 ` Nick Dokos
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