Unexpected output in knitr when using subfigures

Question

I tried to change some of my scripts from sweave to knitr and have found that subfigure failed to render properly when using knitr while they were correct with sweave. I am well aware that knitr offers a way to produce subfigure in knitr header options like in this post, but my question I have several long reports and would like to re-use these code with minimal change. In addition I would like to understand why when using knitr, a simple subfigure example fails.

Example with sweave

In sweave (1) to respect standard knitr output I save the figure in the figure subdirectory, and I create two pdf figures. This is the code for the .Rnw file to be processed using sweave().

\documentclass[a4paper]{article}
\usepackage{graphicx} 
\usepackage{subcaption}
\usepackage{float}
\graphicspath{{figure/}}
\title{test for sweave}
\date{}
\begin{document}
\maketitle

<<multiplefig, echo= FALSE, results=hide>>=
    dir.create("figure",showWarnings = FALSE)
    mapply(function(X){
          pdf(paste0(getwd(),"/figure/fig-",X,".pdf"),height=6,width=6)
          plot(X,main=X)
          dev.off()
        },c(1:2))

@


\begin{figure}[htbp]
 \centering
    \begin{subfigure}[b]{0.45\textwidth}
        \centering
        \includegraphics{fig-1}
        \caption{subcaption1}
    \end{subfigure}%
    ~ 
    \begin{subfigure}[b]{0.45\textwidth}
        \centering
        \includegraphics{fig-2}
        \caption{subcaption2}
    \end{subfigure}
    \caption{Subfigures properly placed side by side in sweave using
    the subfigure command.}
\end{figure}
\end{document}

The output is this :

Example with knitr

With knitr, the output is produced straight from the R code chunk, but when using the subfigure command there is a problem.

\documentclass[a4paper]{article}
\usepackage{subcaption}
\usepackage{float}
\graphicspath{{figure/}}
\title{problem when using knitr}
\date{}
\begin{document}
\maketitle
<<init, include=FALSE>>=
library(knitr) 
@
<<knitrfig, fig.height=6, fig.with=6, include=FALSE>>=
    mapply(function(X)plot(X,main=X),c(1:2))
@



This is where the problem lies
\begin{figure}[htbp]
 \centering
    \begin{subfigure}[b]{0.45\textwidth}
        \centering
        \includegraphics{knitrfig-1}
        \caption{subcaption1}
    \end{subfigure}%
    ~ 
    \begin{subfigure}[b]{0.45\textwidth}
        \centering
        \includegraphics{knitrfig-2}
        \caption{subcaption2}
    \end{subfigure}
    \caption{With knitr the figure is not rendered properly}
\end{figure}
\end{document}

This problem is not linked with the size of the image, I can reproduce it by using the figures fig1 and fig2 produced by the first (sweave) code chunk. I think that some of the packages loaded with knitr might be the cause, and would be much gratefull for a solution to this problem.

score 0 · Accepted Answer · answered Jan 16 '18 at 20:26

I think I understand why.

First I realized that if I add the command \usepackage{Sweave} to the knitr tex output, I no longer had that figure problem. Searching within the sweave code, I've found that it includes the following command :

\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%

In this SO post, David Calisle explains that using

 \setkeys{Gin}{width=0.8\textwidth,height=0.8\textheight,keepaspectratio}

will apply the command to all following \includegraphics.

So I had a restriction on the width of my figures when loading Sweave but I wasn't aware of that, and it no longer worked when I tried to use knitr. Maybe this will be usefull to someone else with the same problems. I will just have to add \setkeys{Gin}{width=0.8\textwidth} to my scripts.

Unexpected output in knitr when using subfigures

Example with sweave

Example with knitr

1 Answers1