knitr - How to align code and plot side by side

Question

is there a simple way (e.g., via a chunk option) to get a chunk\'s source code and the plot it produces side by side, as on page 8 (among others) of this document?

I tri

Answer 1

Well, this ended up being trickier than I'd expected.

On the LaTeX side, the adjustbox package gives you great control over alignment of side-by-side boxes, as nicely demonstrated in this excellent answer over on tex.stackexchange.com. So my general strategy was to wrap the formatted, tidied, colorized output of the indicated R chunk with LaTeX code that: (1) places it inside of an adjustbox environment; and (2) includes the chunk's graphical output in another adjustbox environment just to its right. To accomplish that, I needed to replace knitr's default chunk output hook with a customized one, defined in section (2) of the document's <<setup>>= chunk.

Section (1) of <<setup>>= defines a chunk hook that can be used to temporarily set any of R's global options (and in particular here, options("width")) on a per-chunk basis. See here for a question and answer that treat just that one piece of this setup.

Finally, Section (3) defines a knitr "template", a bundle of several options that need to be set each time a side-by-side code-block and figure are to be produced. Once defined, it allows the user to trigger all of the required actions by simply typing opts.label="codefig" in a chunk's header.

\documentclass{article}

\usepackage{adjustbox}            %% to align tops of minipages
\usepackage[margin=1in]{geometry} %% a bit more text per line

\begin{document}

<<setup, include=FALSE, cache=FALSE>>=
## These two settings control text width in codefig vs. usual code blocks
partWidth <- 45
fullWidth <- 80
options(width = fullWidth)

##  (1) CHUNK HOOK FUNCTION
##   First, to set R's textual output width on a per-chunk basis, we
## need to define a hook function which temporarily resets global R's
## option() settings, just for the current chunk
knit_hooks$set(r.opts=local({
    ropts <- NA
    function(before, options, envir) {
        if (before) {
            ropts <<- options(options$r.opts)
        } else {
            options(ropts)
        }
    }
}))

## (2) OUTPUT HOOK FUNCTION

##   Define a custom output hook function. This function processes _all_
## evaluated chunks, but will return the same output as the usual one,
## UNLESS a 'codefig' argument appeared in the chunk's header.  In that
## case, wrap the usual textual output in LaTeX code placing it in a
## narrower adjustbox environment and setting the graphics that it
## produced in another box beside it.

defaultChunkHook <- environment(knit_hooks[["get"]])$defaults$chunk

codefigChunkHook <- function (x, options) {
        main <- defaultChunkHook(x, options)
        before <-
            "\\vspace{1em}\n
             \\adjustbox{valign=t}{\n
             \\begin{minipage}{.59\\linewidth}\n"
        after <-
            paste("\\end{minipage}}
                   \\hfill
                   \\adjustbox{valign=t}{",
                   paste0("\\includegraphics[width=.4\\linewidth]{figure/",
                           options[["label"]], "-1.pdf}}"), sep="\n")
    ## Was a codefig option supplied in chunk header?
    ## If so, wrap code block and graphical output with needed LaTeX code.
    if (!is.null(options$codefig)) {
      return(sprintf("%s %s %s", before, main, after))
    } else {
      return(main)
    }
}

knit_hooks[["set"]](chunk = codefigChunkHook)


## (3) TEMPLATE
##   codefig=TRUE is just one of several options needed for the
## side-by-side code block and a figure to come out right. Rather
## than typing out each of them in every single chunk header, we
## define a _template_ which bundles them all together. Then we can
## set all of those options simply by typing opts.label="codefig".

opts_template[["set"]](
codefig = list(codefig=TRUE, fig.show = "hide",
               r.opts = list(width=partWidth),
               tidy = TRUE,
               tidy.opts = list(width.cutoff = partWidth)))
@

A chunk without \texttt{opts.label="codefig"} set...
<<A>>=
1:60
@

\texttt{opts.label="codefig"} \emph{is} set for this one

<<B, opts.label="codefig", fig.width=8, cache=FALSE>>=
library(raster)
library(RColorBrewer)

## Create a factor raster with a nice RAT (Rast. Attr. Table)
r <- raster(matrix(sample(1:10, 100, replace=TRUE), ncol=10, nrow=10))
r <- as.factor(r)
rat <- levels(r)[[1]]
rat[["landcover"]] <- as.character(1:10)
levels(r) <- rat

## To get a nice grid...
p <- as(r, "SpatialPolygonsDataFrame")

## Plot it
plot(r, col = brewer.pal("Set3", n=10),
     legend = FALSE, axes = FALSE, box = FALSE)
plot(p, add = TRUE)
text(p, label =  getValues(r))
@

\texttt{opts.label="codefig"} not set, and all settings back to ``normal''.
<<C>>=
lm(mpg ~ cyl + disp + hp + wt + gear, data=mtcars)
@


\end{document}

Answer 2

I see 3 possibilities

• for beamer presentations, I'd go for \begin{columns} ... \end{columns} as well.
• If it is only one such plot: Minipages
• Here I used a table (column code and column result). (This example is "normal" Sweave)

For all three, the chunk options would have include = FALSE, and the plot would "manually" be put to the right place by \includegraphics[]{}.

Answer 3

You can display the text in a 'textplot' from package PerformanceAnalytics or gplots.

(Little) downside: To my knowledge there is no Syntax highlighting possible.

Sample Code:

```{r fig.width=8, fig.height=5, fig.keep = 'last', echo=FALSE}
suppressMessages(library(PerformanceAnalytics))
layout(t(1:2))
textplot('plot(1:10)')
plot(1:10)
```