Knitr: How to make a crossreferences to figures and tables generatrd by code chunks?

Question

I would like to make cross-references to images and tables generated from knitr code chunk in the same way as to standard figures and tables. In a standard figure I use control sequence \label, but i don`t know how to put it into a code chunk. (My document contains also standard figures. Therefore I want to have one numbering of all figures and other one for all tables, no matter how they were generated.)

My code:

\documentclass[a4paper,12pt, english]{article}
\usepackage[colorlinks=true,
            linkcolor=gray,
            urlcolor=blue,
            citecolor=gray,
            ]{hyperref}
\usepackage{graphicx}

\begin{document}
<<chunk_image, results="asis">>=
plot(iris)
@

<<chunk_table, results="asis">>=
library(xtable)
print(xtable(head(iris)))
@

Some text about the image (see \autoref{chunk_image})
\\ Some text about the table (see \autoref{chunk_table})
\end{document}

The outptut I want to get:

Some text about the image (see Figure 1)
Some text about the table (see Table 1)

Answer 1

There are two approaches to this.

Approach 1. Set the label inside TeX, and use R only to generate the body of the figure or table. For example,

\begin{figure}
\begin{center}
<<image,echo=FALSE>>= 
boxplot(na.omit(iris))
@ 
\end{center}
\caption{Iris Boxplot}
\label{fig:iris}
\end{figure}

Note that caption and label are defined inside TeX.

Approach 2. Generate labels and captions inside R, and send them to TeX. For example,

<<table,results='asis', echo=FALSE>>=
library(xtable)
print(xtable(head(iris),caption='Iris table',label='tab:iris'))
@ 

Here we do not put \begin{table}...\end{table}, \caption or \label in TeX file, since xtable does it for us.

Note that knitr generates figure labels for you if you use fig.cap option, for example, the chunk

<<my_chunk, fig.cap='Iris plot'>>=
plot(iris)
@

will have \begin{figure}...\end{figure} inserted with the label fig:my_chunk.

In both cases you can refer to these labels in the usual way:

See Figure~\ref{fig:iris} and Table~\ref{tab:iris}.

You can mix these approaches in the same file, provided that each figure or table uses either the first or the second approach.

Answer 2

I haven't tried kniter and I couldn't compile the code you are providing. Anyways, it happened for me to write some LaTeX command instead of figures on my papers. I hope you are not using something incompatible with figure environment. A simple example can be this code:

\documentclass[a4paper,12pt, english]{article}
\usepackage[colorlinks=true,linkcolor=red,urlcolor=blue,citecolor=gray,]{hyperref}
\usepackage{graphicx}

\begin{document}

\begin{figure*}[t]
    \centerline{ I have some  text here inside figure}
 \caption{Defined coordinate frames for the macro robot.}
 \label{myfig}
\end{figure*}

\begin{table}[t]
    \centerline{ I have some  text here inside table}
    \caption{Defined coordinate frames for the macro robot.}
    \label{mytable}
\end{table}
    Some text about the image (see \autoref{myfig}) \\
    Some text about the table (see \autoref{mytable})   \\
\end{document}

The output is the same as you are talking about: