#+TITLE:     Generating PGF graphics from R in org-babel
#+AUTHOR:    Austin F. Frank
#+EMAIL:     austin.frank@gmail.com
#+DATE:      2009-12-11 Fri
#+LANGUAGE:  en
#+OPTIONS:   H:3 num:nil toc:nil \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+LATEX_HEADER:  \usepackage{tikz} 


Recently a new =R= package, =pgfSweave=, was announced.[fn:1]  This
package boasts a fascinating capability:  generating all R graphics as
\{LaTeX} code that will be typeset using the tikz package and included
as PGF graphics.[fn:2]  This is an appealing option for several
reasons:
  1.  Scaling of size and adjustments of position should be handled
      seamlessly and without loss of resolution
  2.  Colors can be specified identically for graphics and any other
      markup in the $\LaTeX$ document
  3.  Since they're just more $\LaTeX$ code, graphics can be manually
      edited in emacs
  4.  Same fonts will be used for text in figures as are used in the
      text of the document
  5.  $\LaTeX$ markup can be used in figure text
  6.  tikz integrates nicely with Beamer

Given this list of features, I decided to see whether I could get
similar functionality in org-babel.
* R code
** Load =tikzDevice=
   First, we need to load the packages required for producing tikz
   output in =R=.  If all goes well, you should get a message about
   the paths to the various programs required to generate $\LaTeX$
   markup from within =R=.

#+source: load_tikzDevice
#+BEGIN_SRC R :results output :exports both :cache
## I want to show the messages that are generated when the package is
## loaded.  These are printed to the equivalent of stderr, so I have
## to rewrite the `message' function to produce output that I can
## print back later.
tikz.message <-
  capture.output(withCallingHandlers(library(tikzDevice),
                                     message =
                                     function (m) cat(m$message)))

cat(tikz.message, sep="\n")
#+END_SRC

** R example
#+source: lmer_example
#+BEGIN_SRC R :results output :exports both :cache :session
## I use this library all the time
library(lme4)

## here's the standard example
m <- lmer(Reaction ~ Days + (1 | Subject), sleepstudy)
print(m)
#+END_SRC

** Graphics creation
#+source: tikz_example
#+BEGIN_SRC R :results file :exports code :cache :session
library(tikzDevice)
ranef.m <- ranef(m, postVar = TRUE)
tikz(file = "ranef.tex", width=4, height=4)
print(qqmath(ranef.m))
dev.off()
#+END_SRC

#+BEGIN_CENTER
#+CAPTION:  sample graphics
\input{ranef}
#+END_CENTER

* Footnotes

[fn:1] http://thread.gmane.org/gmane.comp.lang.r.packages/351

[fn:2] http://sourceforge.net/projects/pgf/