\name{overview}
\alias{overview}
\title{Draw boxplot, histogram and hierarchical tree of gene expression data}
\description{
Very simple wrapper function that draws a boxplot, histogram and hierarchical tree of expression 
data}
\usage{overview(dataset, labels = NULL, title = "", classvec = NULL, hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree=FALSE)}
\arguments{
   \item{dataset}{A \code{\link{matrix}}, \code{\link{data.frame}}, 
    \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}} or 
    \code{\link[marray:marrayRaw-class]{marrayRaw-class}}.  
     If the input is gene expression data in a \code{\link{matrix}} or \code{\link{data.frame}}. The 
     rows and columns are expected to contain the variables (genes) and cases (array samples) 
     respectively.}
   \item{labels}{Vector, labels to be placed on samples in plots. Default is rownames(dataset).}
   \item{title}{Character, label to be placed on plots. Default is \code{NULL}.}
  \item{classvec}{A \code{factor} or \code{vector} which describes the classes in columns of the
  \code{dataset}. Default is \code{NULL}. If included columns (array samples) on the dendrogram will be coloured by class.}
  \item{hc}{Logical. Draw dendrogram of hierarchical cluster analysis of cases. Default is \code{TRUE}.}
  \item{boxplot}{Logical. Draw boxplot. Default is \code{TRUE}.}
  \item{hist}{Logical. Draw histogram. Default is \code{TRUE}.}
  \item{returnTree}{Logical. Return the hieracrhical cluster analysis results. Default is \code{FALSE}.}
   \item{\dots}{further arguments passed to or from other methods.}
  }
\details{The hierarchical plot is produced using average linkage cluster analysis with Pearson's correlation metric as described by Eisen et al.,1999.}
\value{}
\references{  }
\author{Aedin Culhane}
\note{}
\seealso{See also as \code{\link[graphics:boxplot]{boxplot}}, \code{\link[stats:hclust]{hclust}}, 
\code{\link[graphics:hist]{hist}}}
\examples{
  data(khan)

  logkhan<-log2(khan$train)
  print(class(logkhan))
  overview(logkhan, title="Subset of Khan Train")
  overview(logkhan, classvec=khan$train.classes, labels=khan$train.classes,title="Subset of Khan Train")
  overview(logkhan, classvec=khan$train.classes, labels=khan$train.classes,title="Subset of Khan Train", boxplot=FALSE, his=FALSE)
}
\keyword{hplot}% at least one, from doc/KEYWORDS
\keyword{manip}% __ONLY ONE__ keyword per line