Knitr: Referencing data from a figure later in the paper

Question

I'm working with knitr

Is it possible to reference data from a figure in the paper?

I have a code chunk that produces a figure in the appendix of my paper. I know how to reference the figure itself

"figure 5 shows a histogram..."

with

"figure \ref{fig:hist_fig} shows a histogram..."

and, in the appendix,

\begin{figure}
<<hist_fig, cache=FALSE, echo=F>>=
require(ggplot2)
@
\caption{\label{fig:hist_fig} An example histogram} 
\end{figure}

with another R file that starts with # ---- hist_fig ---- and contains the data that produces the histogram, mean, and variance.

but is it possible to reference data from the figure in the paper as well? For instance "figure 5 has a mean of 6 and a variance of 3."

Would this method work for randomly generated data sets that aren't the same on each run?

Maybe the dependson option would help? – wilx Jul 26 '16 at 11:06 — wilx, Jul 26 '16 at 11:06
@wilx maybe - I'll take a look. Thanks for the suggestion. – RootFAIL Jul 26 '16 at 11:15 — RootFAIL, Jul 26 '16 at 11:15

score 1 · Accepted Answer · answered Jul 26 '16 at 20:22

1

You can cache the later code chunk (cache = TRUE) and use knitr::load_cache() to fetch the object in the chunk. See the help page ?knitr::load_cache for more info.

answered Jul 26 '16 at 20:22

Yihui Xie

2,805

score 1 · Answer 2 · answered Jul 27 '16 at 02:40

Here is a simple but less powerful solution. It would be my preference because it avoids caching (which is very hard to get right every time). The downside is that you have to keep track of the chunks (though if you don't you'll probably get an error).

Note that I'm using assign, which is generally frowned upon. I think it's justified here though.

\documentclass{article}

\begin{document}

<<figure_data>>=
figure_data <- function(.data){
  current_chunk_label <- knitr::opts_current$get(name = "label")
  assign(paste0(current_chunk_label, "_data"),
         list(mean = mean(.data), variance = var(.data)), 
         inherits = TRUE)
}
@

<<hist_fig, fig.show='hide'>>=
library(magrittr)
rnorm(100) %T>%
  figure_data %>%
  hist
@
Figure \ref{fig:hist_fig} shows a histogram with mean \Sexpr{hist_fig_data$mean} 
and variance \Sexpr{hist_fig_data$var}.

\appendix
\begin{figure}
\caption{}\label{fig:hist_fig}
\includegraphics{figure/hist_fig-1}
\end{figure}


\end{document}

Knitr: Referencing data from a figure later in the paper

2 Answers2