Question

I would like to find a way to use the LaTeX \ref{} markup to comment in the R code within a Sweave .Rnw file. Here are two examples, one in print

http://cm.bell-labs.com/cm/ms/departments/sia/project/nlme/UGuide.pdf

and one to use to work with:

The .Rnw file

% File: example.Rnw

\documentclass{article}
\usepackage{fullpage}
\usepackage{graphics}
\usepackage{Sweave} 
\usepackage[margin = 10pt, font=small, labelfont={bf}]{caption}

\begin{document}

Here is an example file to show what I want to do.  I would like to figure out how to use the \LaTeX\ reference command to reference a figure being generated by R code.  Note in the R code, in a comment there is a reference to the figure, but of course the output file shows a verbatim copy of the \LaTeX\ markup.  Does anyone know how to get something for Figure \ref{fig2}?

<< example plot >>=
library(reshape)
library(ggplot2)

n <- 100
lambda <- 1 / 3 
x <- seq(0, qexp(0.999, rate = lambda), length = n)
q1.a <- data.frame(x =   x,
                   f =   dexp(x, rate = lambda),
                   F =   pexp(x, rate = lambda))

q1.a <- melt(q1.a, id.vars = 'x')
g <- ggplot(q1.a) +                                     # Produces \ref{fig1} 
       aes(x = x, y = value) + 
       geom_line() + 
       facet_wrap( ~ variable, scale = "free_y")
ggsave(g, filename = "example1.jpeg")                    
@

\begin{figure}[h]
\centering
\includegraphics[width = 0.48\textwidth]{./example1}
\caption{Exponential Distribution based plots.}
\label{fig1}
\end{figure}

Here is more of what I would like to see:

<< example plot 2 >>=
ggsave(g + geom_point(), filename = "example2.jpeg")    # Produces Figure 2
@

\begin{figure}
\centering
\includegraphics[width = 0.48\textwidth]{./example2}
\caption{Exponential Distribution based plots with points and lines.}
\label{fig2}
\end{figure}

\end{document}

and the pdf is build with the R commands

Sweave(file = 'example.Rnw',
       engine = "R",
       keep.source = 'TRUE',
       echo = 'TRUE',
       results = 'verbatim')

tools::texi2dvi(file  = "example.tex",
                pdf   = TRUE,
                clean = TRUE)

Any insight on how do this would be great.

Answer 1

Here is one way to solve this issue by redefining the Sinput environment in which source code is wrapped by Sweave. By default, it is a simple verbatim environment which is not processed by latex for tokens. The trick is to redefine it to use the alltt environment which allows some tokens to be parsed inside the alltt environment. Note that this might lead to unwanted side effects that I am not aware of, so use with caution!

Here is a reproducible example that works. If you compile it, you will generate a file where ref{fig1} is replaced by the figure number.

\documentclass{article}
\usepackage{Sweave}
\usepackage{alltt}
\renewenvironment{Sinput}{\begin{alltt}}{\end{alltt}}

\begin{document}

In this document, we will create a plot using `R`, and reference its position in 
the source code.

<<produce-plot, results = hide>>=
pdf('example1.pdf')
plot(1:10, 1:10)     # Produces Figure \ref{fig1}
dev.off()
@

\begin{figure}
\includegraphics{example1.pdf}
\caption{Figure 1}
\label{fig1}
\end{figure}

\end{document}