Sec-Plotting.Rnw

\section{Plotting}

<<env, echo=FALSE, massage = FALSE>>=
suppressPackageStartupMessages(library(Biobase))
data(sample.ExpressionSet)
@ 

\begin{frame}
  \begin{itemize}
  \item Scatterplots with \Rfunction{plot}
  \item Boxplots with \Rfunction{boxplot}
  \item Barplots with \Rfunction{barplot}
  \item Histograms with \Rfunction{hist}    
  \item \Rfunction{smoothScatter}        
  \end{itemize}  
\end{frame}

\begin{frame}[fragile]
<<plotcode, eval = FALSE, tidy = FALSE>>=
plot(exprs(sample.ExpressionSet[, 1]), 
     exprs(sample.ExpressionSet[, 2]), 
     log = "xy", 
     xlab = sampleNames(sample.ExpressionSet)[1],
     ylab = sampleNames(sample.ExpressionSet)[2])
abline(0, 1)
grid()
@   
\end{frame}


\begin{frame}[fragile]
  \scriptsize
<<label=plotfig1, echo=FALSE, fig.width=5, fig.height=4, tidy=FALSE, warning = FALSE>>=
plot(exprs(sample.ExpressionSet[, 1]), 
     exprs(sample.ExpressionSet[, 2]), 
     log = "xy", 
     xlab = sampleNames(sample.ExpressionSet)[1],
     ylab = sampleNames(sample.ExpressionSet)[2])
abline(0, 1)
grid()
@
\end{frame}


\begin{frame}[fragile]
  To create subplots, one can use \Rfunction{par(mfrow = c(2,2))}, \Rfunction{layout}, or (for scatterplots)
<<plotcode0, eval = FALSE, tidy = FALSE>>=
pairs(log2(exprs(sample.ExpressionSet)[, 1:4]),
      pch = 19,
      col = "#0000FF20")
@   
\end{frame}

\begin{frame}[fragile]
  \scriptsize
<<label=plotfig2,echo=FALSE,fig.width=3.5,fig.height=3.5,tidy=FALSE, warning = FALSE>>=
pairs(log2(exprs(sample.ExpressionSet)[, 1:3]),
      pch = 19,
      col = "#0000FF20")
@
\end{frame}

\begin{frame}[fragile]
<<plotcode1, eval = FALSE>>=
boxplot(log2(exprs(sample.ExpressionSet)))
@   
\end{frame}


\begin{frame}[fragile]
  \scriptsize
<<label=plotfig3,echo=FALSE,fig.width=5,fig.height=4,tidy=FALSE>>=
boxplot(log2(exprs(sample.ExpressionSet)))
@
\end{frame}

%% \begin{frame}[fragile]
%% <<plotcode2, eval = FALSE>>=
%% smoothScatter(log2(exprs(sample.ExpressionSet)[, 1:2]))
%% @   
%% \end{frame}

\begin{frame}[fragile]
  \scriptsize
<<label=plotfig4,echo=TRUE,fig.width=5,fig.height=4,tidy=FALSE, warning = FALSE, message = FALSE>>=
smoothScatter(log2(exprs(sample.ExpressionSet)[, 1:2]))
@
\end{frame}

\begin{frame}
  \begin{block}{References}
    We have not covered \Rpackage{lattice} and \Rpackage{ggplot2}.
  \end{block}
  \begin{block}{References}
    \begin{itemize}
    \item \url{http://gallery.r-enthusiasts.com/allgraph.php}
    \item R Graphics manual: \url{http://rgm3.lab.nig.ac.jp/RGM/r_image_list}
    \item \url{http://www.cookbook-r.com/Graphs/} (ggplot2)
    \end{itemize}
  \end{block}
\end{frame}