HoExample4.Rnw

\documentclass{beamer}
\usepackage{beamerthemeshadow}
\usepackage{url,graphics,amsmath,pstricks,hyperref,times,color}
\usepackage{graphicx}
\usepackage{Sweave}
\usepackage{amscd}
\usepackage[tableposition=top]{caption}
\usepackage{ifthen}
\usepackage[utf8]{inputenc}

\newcommand{\R}{\textsf{R}}
\def\be{\begin{scriptsize}}
\def\ee{\end{scriptsize}}
\def\bi{\begin{itemize}}
\def\ei{\end{itemize}}  
\def\bv{\begin{verbatim}}
\def\ev{\end{verbatim}}
\setbeamertemplate{footline}{\insertpagenumber/\insertpresentationendpage} 

%%%%%%%%% heart shape
\usepackage{shapepar}


\renewcommand{\topfraction}{.85} 
\renewcommand{\bottomfraction}{.7}
\renewcommand{\textfraction}{.15} 
\renewcommand{\floatpagefraction}{.66}
\renewcommand{\dbltopfraction}{.66} 
\renewcommand{\dblfloatpagefraction}{.66}

\sloppy
\raggedbottom
\addtolength{\topskip}{0pt plus 8pt}

\newcommand\configpar[6]{\par\penalty-50
 \vskip 0pt plus 12pt \penalty 50 \vskip 0pt plus -12pt
 \begingroup\samepage
 \paragraph*{\textbackslash #1} #2\unskip\strut\\*
 \begin{tabular}{@{}p{.15\linewidth}@{}p{.85\linewidth}@{}}
 Type: \ & \rightskip\fill #3\\
 Default: \ & \rightskip\fill #4\\
 Set with: \ & \rightskip\fill #5\\
 Example: \ & \rightskip\fill #6
 \end{tabular}
 \par \endgroup
}

% Code from: underscore.sty     12-Oct-2001   Donald Arseneau   asnd@triumf.ca
% Make the "_" character print as "\textunderscore" in text.

\makeatletter
\begingroup
 \catcode`\_=\active
 \gdef_{% \relax % No relax gives a small vulnerability in alignments
   \ifx\if@safe@actives\iftrue % must be outermost test!
      \string_%
   \else
      \ifx\protect\@typeset@protect
         \ifmmode \sb \else \BreakableUnderscore \fi
      \else
         \ifx\protect\@unexpandable@protect \noexpand_%
         \else \protect_%
      \fi\fi
    \fi}
\endgroup




\title{Making Nice Slides using Beamer and Sweave}
\author[Yen-Yi Ho]{Yen-Yi Ho}
\institute[University of Minnesota]{
  Division of Biostatistics\\
  School of Public Health \\
    University of Minnesota
}

\date{}

\begin{document}
\SweaveOpts{concordance=TRUE}

\frame{
  \titlepage
}

<<options, echo=FALSE, results=hide>>=
library(tools)
options(width=55)
@ 

\section{Beamer}

\begin{frame}\frametitle{Syntax in Beamer}
$\backslash$documentclass\{beamer\} \\
$\backslash$usepackage\{beamerthemeshadow\} \\
$\backslash$title\{Mytitle\}\\
\vspace{0.2in}
$\backslash$begin\{document\} \\
$\backslash$begin\{frame\} \\
 $\backslash$titlepage \\
$\backslash$end\{frame\} \\
\vspace{0.2in}
$\backslash$begin\{frame\} \\
Content for Slide 1  \\
$\backslash$end\{frame\} \\
\vspace{0.2in}
$\backslash$end\{document\} \\
\end{frame}

\subsection{Pause}
\begin{frame}\frametitle{Lists with Pause}
\begin{itemize}
\item Introduction to  \LaTeX \pause 
\item Course 2 \pause 
\item Termpapers and presentations with \LaTeX \pause 
\item Beamer class
\end{itemize} 
\end{frame}

\subsection{Table} 

\begin{frame}\frametitle{Tables}

%<<analyticData, results=hide, print=FALSE>>=
%a1<-paste(sample(LETTERS,6), collapse="")
%a2<-paste(sample(LETTERS,6), collapse="")
%@ 
\begin{tabular}{|c|c|c|}
\hline
\textbf{Date} & \textbf{Instructor} & \textbf{Title} \\
\hline
WS 04/05 & John Mich & First steps with  \LaTeX  \\
\hline
SS 05 & Yen-Yi Ho & \LaTeX \ Course serial \\
\hline
\end{tabular}
\end{frame}

\subsection{Splitting Screen}
\begin{frame}\frametitle{Splitting Screen}
\begin{columns}
\begin{column}{5cm}
\begin{itemize}
\item Beamer 
\item Beamer Class 
\item Beamer Class Latex 
\end{itemize}
\end{column}
\begin{column}{5cm}
\begin{tabular}{|c|c|}
\hline
\textbf{Instructor} & \textbf{Title} \\
\hline
John &  \LaTeX \ Course 1 \\
\hline
Anding  &  Course serial  \\
\hline
\end{tabular}
\end{column}
\end{columns}
\end{frame}

\subsection{Plain} 
\begin{frame}[plain]
\frametitle{Tables}
\begin{tabular}{|c|c|c|}
\hline
\textbf{Date} & \textbf{Instructor} & \textbf{Title} \\
\hline
WS 04/05 & Yen-Yi Ho & First steps with  \LaTeX  \\
\hline
SS 05 & Mica Shen & \LaTeX \ Course serial \\
\hline
\end{tabular}
\end{frame}

\subsection{Animation}


<<h1, fig=TRUE, include=FALSE, echo=FALSE, eps=true, results=hide,width=6, height=6>>=
##I use include=FALSE and then use latex to put the figure exactly where I want
require(affy) || {
	message("package not available. downloading from Bioconductor")
	source("http://www.bioconductor.org/biocLite.R")
	biocLite("affy", type="source")
}
require(gplots) || {
	message("package not available. downloading from Bioconductor")
	source("http://www.bioconductor.org/biocLite.R")
	biocLite("gplots", type="source")
}
require(SpikeIn) || {
	message("package not available. downloading from Bioconductor")
	source("http://www.bioconductor.org/biocLite.R")
	biocLite("SpikeIn", type="source")
}


library(affy)
library(gplots)
library(SpikeIn)
data(SpikeIn)
pms <- SpikeIn@pm

 # just the data, scaled across rows
 heatmap.2(pms, col=rev(heat.colors(16)), main="SpikeIn.pm", 
              xlab="Relative Concentration", ylab="Probeset", 
              scale="row")
@ 
<<h2, fig=TRUE, include=FALSE, echo=FALSE, eps=true, width=6, height=6>>=
 # fold change vs "12.50" sample
 data <- pms / pms[, "12.50"]
 data <- ifelse(data>1, data, -1/data)
 heatmap.2(data, breaks=16, col=redgreen, tracecol="blue", 
               main="FoldChange", 
               xlab="Relative Concentration", ylab="Probeset")
@ 


\begin{frame}
\frametitle{Animation}
\begin{columns}
\begin{column}{2.5cm}
\begin{itemize}
\item<1-> subject 1
\item<3-> subject 2
\end{itemize}
\vspace{3cm} 
\end{column}
\vspace{-0.2in}
\begin{column}{7.5cm}
\begin{overprint}
\includegraphics<2>{HoExample4-h1}
\includegraphics<4>{HoExample4-h2}
\end{overprint}
\end{column}
\end{columns}
\end{frame}



\subsection{Love Letter}
\begin{frame}\frametitle{Love Letter Too}
{\small $\backslash$heartpar\{\}}\\
\vspace{0.1in}
\def~{\,}
\heartpar{%
\tiny
\mbox{}If I speak in the tongues of men or of angels, but do not have love, I am only a resounding gong or a clanging cymbal. If I have the gift of prophecy and can fathom all mysteries and all knowledge, and if I have a faith that can move mountains, but do not have love, I am nothing.  If I give all I possess to the poor and give over my body to hardship that I may boast, but do not have love, I gain nothing. Love is patient, love is kind. It does not envy, it does not boast, it is not proud.  It does not dishonor others, it is not self-seeking, it is not easily angered, it keeps no record of wrongs.  Love does not delight in evil but rejoices with the truth. It always protects, always trusts, always hopes, always perseveres.} 
\vspace{0.1in}
{\scriptsize More Beamer TeX examples and templates : \url{http://www.informatik.uni-freiburg.de/~frank/ENG/latex-course/latex-course-3/latex-course-3_en.html}}
\end{frame}



\section{Adding Sweave} 
\subsection{Literate Programming}
\begin{frame}
  Literate programming means that text, data, and computer code are
  interwoven in a single self-contained document.
\end{frame}

\begin{frame}
  \frametitle{This Is Not Literate Programming}
  
  A research document involving multiple files with figures and tables
  cut and paste from various places.  For instance,
  
  \begin{itemize}
  \item a stata do-file
    
  \item an excel spreadsheet with results
    
  \item an excel spreadsheet with data
    
  \item a directory with filenames like ``old.doc'' and ``new.doc''
    
  \item a word document with tables and figures cut and paste from
    various places
      
  \end{itemize}
  
  *Changes to the stata do-file are not automatically propogated to
  the excel spread-sheet or to the Word document.
  
\end{frame}    

\subsection{Why Sweave}
\begin{frame}
  \frametitle{Why You Should Use Literate Programming}
  
  \begin{itemize}
    
  \item Reproducible research
    
  \item Dynamic reports
    
  \item \textsf{R} Package vignettes: R vignettes are usually developed using Sweave    
  \end{itemize}
  
\end{frame}
  
 \subsection{How Sweave Works} 
\begin{frame}[containsverbatim]
  \frametitle{Literate programming for \R{} uses Sweave}
  \begin{small}
    Essentially requires a single source document -- a '.Rnw' file.
  \end{small}

$$
\begin{CD}
   \texttt{*.Rnw}
   @>\texttt{Sweave}>>
   \texttt{*.tex}
   @>\texttt{latex}>>
   \texttt{*.dvi}
   @>\texttt{xdvi}>>
   \text{view of document}
\end{CD}
$$

% \begin{center}
% \includegraphics[scale=0.5]{processingNoWeb.pdf}
 %\end{center}
  \be
  see \url{http://www.bias-project.org.uk/Rpackages_course/intro_Sweave.pdf}
  \ee
\end{frame}

\begin{frame}[containsverbatim]
  \frametitle{This Presentation}
  
  If you have beamer and tex installed, try reproducing this talk:
\be  
<<sweaveThisTalk, eval=FALSE>>=
Sweave("HoExample4.Rnw")
Sys.setenv(PATH=paste(Sys.getenv("PATH"),"/usr/texbin",sep=":"))
texi2dvi("HoExample4.tex", pdf=T, quiet=F)
@ %def 
\ee
Tricks for compiling Rnw file:
\begin{itemize}
\item If using older versions of R,\\
{\tt >Sweave("HoExample4.Rnw")} sometimes gives error messages saying some packages do not exist. Type \\
{\tt > biocLite("TheMissingPackage")} to solve the problem.  
\item If having no luck in \\
{\tt >texi2dvi("HoExample4.tex", pdf=T, quiet=F)}, then open your favorite TeX editor and run TeX and Dvi to compile ``HoExample4.tex"
\end{itemize}
\end{frame}

\begin{frame}\frametitle{Syntax using Beamer and Sweave}
\small
$\backslash$documentclass\{beamer\} \\
$\backslash$usepackage\{beamerthemeshadow\} \\
$\backslash$usepackage\{Sweave\} \\
$\backslash$begin\{document\} \\
$\backslash$begin\{frame\} \\
\ \ \ \ \ Content for Slide 1  \\
$\backslash$end\{frame\} \\
\textcolor{blue}{$\ll$ \ \ \ \ \ $\gg$=} \\
\textcolor{blue}{my R code chunk} \\
\textcolor{blue}{$@$} \\
$\backslash$begin\{frame\} \\
\ \ \ \ \ \ Content for Slide 2  \\
$\backslash$end\{frame\} \\
\vspace{0.2in}
$\backslash$end\{document\} \\
\end{frame}

\begin{frame}
  \frametitle{Code Chunk Options}

  \begin{itemize}
  \item \texttt{eval(TRUE, or FALSE)} \\
   Whether the R chunk is run
  \item \texttt{echo(TRUE, FALSE)}  \\
  Whether the R chunk is shown in the \LaTeX\ file
  \item \texttt{results(verbatim, hide, tex)} \\
  Type of output used to show the printed results produced by the R code. 
 \item  \texttt{fig(TRUE, FALSE)} \\
  Whether the output is a figure. By default, PDF files are produced. 
  \item $\ll$\texttt{figname, fig=TRUE, include=FALSE}$\gg$ \\
  \end{itemize}
  
  See the \texttt{HoExample4.Rnw} for examples.

\end{frame}

\begin{frame}[containsverbatim]
  \frametitle{Extracting Code Chunks}
  
  To extract code chunks from a .Rnw file:
  
<<stangle, eval=FALSE>>=
Stangle("HoExample4.Rnw")
@ %def 

This command generates the file \texttt{HoExample4.R} containing the
code chunks used in this presentation.

\end{frame}

\subsection{Dynamic Reports}
\begin{frame}[containsverbatim]
  \frametitle{Dynamic Reports}
\be  
<<analyticData, results=hide>>=
require(geneplotter) || {
	message("package not available. downloading from Bioconductor")
	source("http://www.bioconductor.org/biocLite.R")
	biocLite("geneplotter", type="source")
}
x1  <- matrix(rnorm(1e4), ncol=2)
x2  <- matrix(rnorm(1e4, mean=3, sd=1.5), ncol=2)
x   <- rbind(x1,x2)
@ 

<<smoothScatter, fig=TRUE, include=FALSE, echo=TRUE, eps=true, width=7, height=7>>=
##I use include=FALSE and then use latex to put the figure exactly where I want
par(mfrow=c(2,2), las=1)
par(mar=c(2,2,2,1))
smoothScatter(x, nrpoints=0)
smoothScatter(x)
smoothScatter(x,nrpoints=Inf,colramp=colorRampPalette(RColorBrewer::brewer.pal(9, "YlOrRd")),bandwidth=1)  
colors  <- densCols(x)
plot(x, col=colors, pch=20)
@ 
\ee
  
\end{frame}

\begin{frame}[plain]
  \frametitle{Interweaving text, \R{} code, and figures}
  \begin{small}
    Any changes to the preceding code will be propagated to this
    figure automatically.
  \end{small}
 \vspace{-0.2in}
\begin{center}
\includegraphics[width=0.6\textwidth]{HoExample4-smoothScatter}
\end{center}
\end{frame}

\begin{frame}
  \frametitle{Many public resources }
  
  Key words for google: reproducible research, Sweave
  
\end{frame}




\end{document}