[Tex/LaTex] How to get correct dimensions for a ggplot2 plot in beamer

beamerrsweave

I have a beamer presentation made with Sweave that I'm preparing and was wanting to place some ggplot2 graphs in but the aspect ratio does not seem to come out correct. This is what is in my Rnw file.

\begin{frame}[containsverbatim]
\frametitle{Basic Workflow}\begin{itemize}
\item Start R (Start > All Programs > R > R x64 2.12.0 )\\
\item Load Packages
<<>>=
library(ggplot2)
library(MASS)
@
\item Load Data
<<>>=
data(iris) # or read.csv/read.table/etc.
head(iris[,3:5],n=3)
@
\item Graph Data
<<>>=
qplot(Petal.Length,Petal.Width,color=Species, data=iris)->p
@
\end{itemize}\end{frame}
\begin{frame}{Basic Workflow, Cont.}
<<fig=T,echo=F>>=
show(p)
@
\end{frame}

what comes out is a graph with the bottom cut off that takes up the left half of the page.

Best Answer

I find this a big pain. I have arrived at doing something like

% one-column
\SweaveOpts{height=5,width=8,echo=FALSE}
\setkeys{Gin}{width=4in}

% two-column
\SweaveOpts{echo=FALSE,height=5,width=5}
\setkeys{Gin}{width=2.25in}

Unfortunately, I don't know of a nice way to incorporate this into a LaTeX command; if I pack these into \onecolumnfig{} or \twocolumnfig{} LaTeX macros, Sweave doesn't see them (because they don't get expanded until after Sweave has processed the file).

Duncan Murdoch has provided various bits of useful information on this topic on the R list:

here and here, for example (results of googling "murdoch sweave setkey")

etc.

edit: the answer now, I think, is "use knitr" instead ( http://yihui.name/knitr/ ) -- it allows an out.width="0.8\\textwidth" (for example) specification in the chunk options.

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[Tex/LaTex] FancyVerb error for Sweave output in Beamer

From the beamer manual (section 12.9 Verbatim and Fragile Text in version 3.10):

If you wish to use a {verbatim} environment in a frame, you have to add the option [fragile] to the {frame} environment. In this case, you really have to use the {frame} environment (not the \frame command) and the \end{frame} must be alone on a single line.

So all you have to do is to replace \begin{frame} by \begin{frame}[fragile].

[Tex/LaTex] Sweave, Beamer and ggplot2

Here is an example where I shamelessly copied some R code from Cross-Validated. It can be compiled in many ways, but personally I used

R CMD Sweave 1.Rnw
pdflatex 1.tex

where 1.Rnw actually reads:

\documentclass[a4paper,11pt]{article}

\title{A sample Sweave demo}
\author{Author name}
\date{}

\begin{document}

\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,strip.white=all}
\SweaveOpts{prefix=TRUE,prefix.string=fig-,include=TRUE}
\setkeys{Gin}{width=0.6\textwidth}

\maketitle

<<echo=false>>=
set.seed(101)
library(ggplot2)
library(ellipse)
@

<<>>=
n <- 1000
x <- rnorm(n, mean=2)
y <- 1.5 + 0.4*x + rnorm(n)
df <- data.frame(x=x, y=y)

# take a bootstrap sample
df <- df[sample(nrow(df), nrow(df), rep=TRUE),]

xc <- with(df, xyTable(x, y))
df2 <- cbind.data.frame(x=xc$x, y=xc$y, n=xc$number)
df.ell <- as.data.frame(with(df, ellipse(cor(x, y), 
                                         scale=c(sd(x),sd(y)), 
                                         centre=c(mean(x),mean(y)))))
p1 <- ggplot(data=df2, aes(x=x, y=y)) + 
  geom_point(aes(size=n), alpha=.6) + 
  stat_smooth(data=df, method="loess", se=FALSE, color="green") + 
  stat_smooth(data=df, method="lm") +
  geom_path(data=df.ell, colour="green", size=1.2)
@

\begin{figure}
  \centering
<<fig=true,echo=false>>=
print(p1)
@
\caption{Here goes the caption.}
\label{fig:p1}
\end{figure}

\end{document}

With Beamer, you just have to replace the first line with

\documentclass[t,ucs,12pt,xcolor=dvipsnames]{beamer}

or add whatever customizations you want, replace \maketitle with something like \frame{\titlepage}, and then enclose every code chunks with a \begin{frame}[fragile] ... \end{frame} statement. Compilation goes the same way as aforementioned.

Code chunks can be customized using, e.g.

\DefineVerbatimEnvironment{Sinput}{Verbatim}
{formatcom = {\color{Sinput}},fontsize=\scriptsize} 
\DefineVerbatimEnvironment{Soutput}{Verbatim}
{formatcom = {\color{Soutput}},fontsize=\footnotesize}
\DefineVerbatimEnvironment{Scode}{Verbatim}
{formatcom = {\color{Scode}},fontsize=\small}

It requires fancyvrb and needs to be somewhere after the \begin{document}. Personally, I hold in an external configuration file, among other stuff,

\definecolor{Sinput}{rgb}{0.75,0.19,0.19}
\definecolor{Soutput}{rgb}{0,0,0}
\definecolor{Scode}{rgb}{0.75,0.19,0.19}

Here is a snapshot:

enter image description here

Best Answer

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[Tex/LaTex] FancyVerb error for Sweave output in Beamer

[Tex/LaTex] Sweave, Beamer and ggplot2

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