knitr how to label and call a figure number in a text

Question

As a knitr beginner I don't know how to label a figure and call it.

For my first figure I've tried the following code witouth succes...

<<fig.cap="Dendrogram of GDP (2000-2012)",fig.lp="fig:test">>=  
plot(HClust.1, main= "Cluster Dendrogram GDP")
@

As you can see the figure \ref{fig:test} shows that...

But after compilation I get figure ?? instead figure 1 ...

Answer 1

fig.lp is not the label of the figure, it is the prefix that is used to create the label. From the description of knitr options

fig.lp: ('fig:'; character) label prefix for the figure label to be used in \label{}; the actual label is made by concatenating this prefix and the chunk label, e.g. the figure label for <<foo-plot>>= will be fig:foo-plot by default

If you don't give your chunks names, they will get a default name such as unnamed-chunk-1 where the number depends on where it is in the file (and so would make for a bad label to target).

Additionally, to get the graphics into a figure environment, you need to give it a caption. Again from the options description

fig.cap: (NULL; character) figure caption to be used in a figure environment in LaTeX (in \caption{}); if NULL or NA, it will be ignored, otherwise a figure environment will be used for the plots in the chunk (output in \begin{figure} and \end{figure})

Without this there is no figure environment and therefore no \label{} created.

Putting this together, here is a MWE:

\documentclass{article}
\begin{document}

<<myfig, fig.cap=''>>=
plot(1:10)
@

As you can see the figure \ref{fig:myfig} shows that...

\end{document}

This creates a .tex file, the relevant (but incomplete) excerpt of which is

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlfunctioncall{plot}(1:10)
\end{alltt}
\end{kframe}\begin{figure}[]

\includegraphics[width=\maxwidth]{figure/myfig} \caption[]{\label{fig:myfig}}
\end{figure}


\end{knitrout}


As you can see the figure \ref{fig:myfig} shows that...

You can see that the \label{} and \ref{} match up now.

See also more discussion about this in a related Stack Overflow question.