%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{10 Visualization in R -- Slides}

\documentclass[xcolor=dvipsnames]{beamer}

\usepackage{BioconductorSlides}
\hypersetup{colorlinks,linkcolor=,urlcolor=Blue}
\AtBeginSection[]
{
  \begin{frame}<beamer>{Outline}
    \tableofcontents[currentsection]
  \end{frame}
}

\begin{document}

<<knitr-settings, echo=FALSE>>=
library(knitr)
opts_chunk$set(tidy=FALSE)
@ 

\title{Visualization}
\author{Martin Morgan (\href{mailto:mtmorgan@fhcrc.org}{mtmorgan@fhcrc.org}) \\
  Fred Hutchinson Cancer Research Center \\
  Seattle, WA}
\date{7 February 2014}
\maketitle

\begin{frame}[fragile]{Visualization}
  \begin{columns}[t]
    \column{.5\textwidth}
    General
    \begin{itemize}
    \item Base graphics
    \item \Rpkg{lattice}
    \item \Rpkg{ggplot2}
    \end{itemize}
    \column{.5\textwidth}
    \Bioconductor
    \begin{itemize}
    \item \Biocpkg{Gviz}, \Biocpkg{ggbio}
    \item \Biocpkg{Rgraphviz}, \Biocpkg{RCytoscape}, \Biocpkg{RedeR}
    \end{itemize}
    Interactive
    \begin{itemize}
    \item \Rpkg{shiny}!
    \end{itemize}
  \end{columns}
  \href{http://accidental-art.tumblr.com/archive}{Accidental aRt}
\end{frame}

\begin{frame}[fragile]{Base graphics}
  \begin{columns}[t]
    \column{.5\textwidth}
    One plot
    \begin{itemize}
    \item Start a \Rfunction{plot}, \Rfunction{matplot},
      \Rfunction{hist}, \Rfunction{boxplot}, \ldots, specifying
      options
    \item Add \Rfunction{legend}, \Rfunction{points}, \ldots
    \item Help: \Rcode{?plot}, \Rcode{?par}
    \end{itemize}
    \column{.5\textwidth}
    Several plots
    \begin{itemize}
    \item Layout with \Rcode{par(mfcol=c(1, 2))}, \Rcode{screen}, \ldots
    \item Create single plots
    \item Restore original \Rcode{par} settings
    \end{itemize}
  \end{columns}
  \bigskip\par
\end{frame}

\begin{frame}[fragile]{Base graphics}
<<exmaple-data-input, echo=FALSE>>=
fl <- system.file(package="SummerX", "extdata", "abc.csv")
stopifnot(file.exists(fl))
abc <- read.csv(fl, row.names=1)
fl <- system.file(package="SummerX", "extdata", "BRFSS-subset.csv")
stopifnot(file.exists(fl))
brfss <- read.csv(fl)
@ 
<<example-data, eval=FALSE>>=
fileName <- file.choose()  # 'abc.csv'
abc <- read.csv(fileName, row.names=1)
@ 
  \begin{columns}
    \column{.5\textwidth}
<<ShortRead-vis, eval=FALSE, tidy=FALSE>>=
## Create a plot from a
## matrix
matplot(t(abc), type="l",
  lty=1, lwd=3, 
  xlab="Cycle",
  ylab="Count",
  cex.lab=2)
## Add a legend
legend("topright", 
  legend=rownames(abc),
  lty=1, lwd=3, col=1:5,
  cex=1.8)
@     
    \column{.5\textwidth}
    \includegraphics[width=\textwidth]{figures/abc}
  \end{columns}
\end{frame}

\begin{frame}[fragile]{Base graphics}
  Data: US Center for Disease Control's Behavioral Risk
  Factor Surveillance System (\href{http://www.cdc.gov/brfss/}{BRFSS})
<<brfss-base-input-in, echo=FALSE>>=
fl <- system.file(package="SummerX", "extdata", "BRFSS-subset.csv")
brfss <- read.csv(fl)
brfss2010 <- brfss[brfss$Year == "2010",]
@ 
<<brfss-base-input, eval=FALSE>>=
brfss <- read.csv(file.choose()) # 'BRFSS-subset.csv'
brfss2010 <- brfss[brfss$Year == "2010",]
@ 
Plot
<<brfss-base-plot, eval=FALSE>>=
## set layout, capture old options
opar <- par(mfcol=c(1, 2))
plot(sqrt(Weight) ~ Height, 
    brfss2010[brfss2010$Sex == "Female", ],
    main="2010, Female")
plot(sqrt(Weight) ~ Height, 
    brfss2010[brfss2010$Sex == "Male", ],
    main="2010, Male")
## restore old options
par(mfcol=c(1, 1))
@ 
\end{frame}

\begin{frame}{Base graphics}
\includegraphics[width=\textwidth]{figures/brfss-base}
\end{frame}

\begin{frame}{\Rpkg{lattice} graphics}
  \begin{itemize}
  \item Main functions like \Rfunction{xyplot}, \Rfunction{dotplot},
    \Rfunction{contourplot}
  \item `Panel' functions that do the work, e.g.,
    \Rfunction{panel.xyplot}, \Rfunction{panel.violin}
  \item Help: \Rcode{?xyplot} for working with the plot overall,
    \Rcode{?panel.xyplot} (and similar) for individual panels.
  \end{itemize}
\end{frame}

\begin{frame}[fragile]{\Rpkg{lattice} graphics}
<<brfss-input-in, echo=FALSE>>=
fl <- system.file(package="SummerX", "extdata", "BRFSS-subset.csv")
brfss <- read.csv(fl)
@ 
<<brfss-input, eval=FALSE>>=
brfss <- read.csv(file.choose()) # 'BRFSS-subset.csv'
@ 
<<lattice, eval=FALSE>>=
library(lattice)
xyplot(sqrt(Weight) ~ Height | Sex, brfss2010)
@   
\includegraphics[width=\textwidth]{figures/brfss-xyplot}
\end{frame}

\begin{frame}[fragile]{\Rpkg{lattice} graphics}
<<lattice-violin, eval=FALSE>>=
bwplot(sqrt(Weight) ~ factor(Year) | Sex, brfss,
    panel=panel.violin)
@   
\includegraphics[width=\textwidth]{figures/brfss-violin}
\end{frame}

\begin{frame}{\Rpkg{ggplot2} graphics}
  \begin{itemize}
  \item Create a plot with \Rfunction{ggplot}
  \item Add \emph{layers} (e.g., \Rfunction{geom\_density} and
    \emph{aesthetics} (e.g., \Rfunction{aes})
  \end{itemize}
\end{frame}

\begin{frame}[fragile]{\Rpkg{ggplot2} graphics}
<<ggplot2-input-in, echo=FALSE>>=
fl <- system.file(package="SummerX", "extdata", "BRFSS-subset.csv")
brfss <- read.csv(fl)
brfss2010 <- brfss[brfss$Year == "2010",]
@ 
<<ggplot2-input, eval=FALSE>>=
brfss <- read.csv(file.choose()) # 'BRFSS-subset.csv'
brfss2010 <- brfss[brfss$Year == "2010",]
@ 
<<ggplot2-density, eval=FALSE>>=
library(ggplot2)
ggplot(brfss2010) + geom_density(alpha=.2) + 
    aes(sqrt(Weight), fill=Sex)
@   
\includegraphics[width=\textwidth]{figures/brfss-geom_density}
\end{frame}

\begin{frame}{Genomic Visualization}
  \begin{itemize}
  \item Very flexible base, \Rpackage{lattice}, and \Rpkg{ggplot2}
    facilities
  \item Ranges and genomes: \Biocpkg{Gviz}, \Biocpkg{ggbio}
  \item Graphs and networks: \Biocpkg{Rgraphviz}, \Biocpkg{RCytoscape}
  \end{itemize}
\end{frame}

\begin{frame}[fragile]{Interactive Visualization}
  \Rpkg{shiny} provides an easy way to create interactive
  graphics. Explore the \emph{Volcano!} application developed in class
  through the source code in the package.
<<shiny, eval=FALSE>>=
system.file(package="SummerX", "shiny")
@ 
\end{frame}

\end{document}