knitr plotting code chunks to be seen and run

Question

I've been trying to solve the following problem using knitr . In \\LaTeX I wish to define a chunk (once) called myplot . Then I want to say something such as:

The code

<<myplot, tidy = FALSE>>=
plot(runif(9), runif(9),
     xlab = "x",
     ylab = "y",)
@

results in Figure~\\ref{fig:myownlabel} .

\begin{figure}[hh]
\begin{center}
<<myplotfig, out.width='.50\\linewidth', width=6.6, height=4.8, echo=FALSE>>=
par(las = 1, mfrow = c(1, 1), mar = c(5, 4, 1, 1)+0.1)
<<myplot>>
@
\caption{
I insist to have the caption in \LaTeX.
\label{fig:myownlabel}
}
\end{center}
\end{figure}

I know how to do it in Sweave but cannot seem to do it in knitr . That is, the code chunk is seen by the reader. Can you give me any suggestions? Thanks in advance. Thomas

Answer 1

This is one difference between knitr and Sweave: Sweave does not keep plots by default (unless you specify fig=TRUE ), but knitr does (unless you really do not want them, using fig.keep='none' ).

<<myplot, tidy = FALSE, fig.keep = 'none'>>=
plot(runif(9), runif(9),
     xlab = "x",
     ylab = "y",)
@

\begin{figure}[hh]
\begin{center}
<<myplotfig, out.width='.50\\linewidth', fig.width=6.6, fig.height=4.8, echo=FALSE>>=
par(las = 1, mfrow = c(1, 1), mar = c(5, 4, 1, 1)+0.1)
<<myplot>>
@
\caption{
I insist to have the caption in \LaTeX.
\label{fig:myownlabel}
}
\end{center}
\end{figure}

Although the problem has been solved so far, I have a few other comments:

1. when you use knitr ( >= 1.1 ), you should be able to see a warning about the syntax of your code chunks, and you are required to call Sweave2knitr() to fix the problems; you will realize width and height are not valid chunk options in knitr (use fig.width and fig.height ); see here for more information
2. for the chunk myplot , I would use eval=FALSE because you probably do not want to evaluate the code twice;

3. with knitr , you can actually do everything through chunk options, eg

    <<myplot, tidy=FALSE, eval=FALSE, echo=-1>>= @ <<myplot, out.width='.5\\\\linewidth', fig.width=6.6, fig.height=4.8, fig.align='center', echo=FALSE, fig.pos='hh', fig.cap='I insist to have the caption in \\\\LaTeX.'>>= par(las = 1, mfrow = c(1, 1), mar = c(5, 4, 1, 1)+0.1) plot(runif(9), runif(9), xlab = "x", ylab = "y",) @ 

   this gives you both the center and figure environments, and produces a label fig:myplot automatically.