\name{arrayPlot}
\alias{arrayPlot}
\alias{arrayPlot.default}
\alias{arrayPlot.arrayCGH}
\encoding{latin1}
\title{Spatial image of microarray spots statistic}
\description{
The function \code{arrayPlot} creates spatial images of shades of gray or colors that correspond to the values of a statistic for each spot on the array. The statistic can be the intensity log-ratio, a spot quality measure (e.g. spot size or shape), or a test statistic. This function can be used to explore whether there are any spatial effects in the data, for example, print-tip or cover-slip effects.
}
\usage{
\method{arrayPlot}{default}(Statistic, Col, Row,
                  ArrCol, ArrRow, SpotCol, SpotRow,
                  mediancenter=FALSE,
                  col=myPalette("green", "red", "yellow"),
                  contour=FALSE, nlevels=5,
                  zlim=NULL, bar=c("none", "horizontal", "vertical"),
                  layout=TRUE, ...) 

\method{arrayPlot}{arrayCGH}(arrayCGH, variable,
                   mediancenter=FALSE,
                   col=myPalette("green", "red", "yellow"),
                   contour=FALSE, nlevels=5,
                   zlim=NULL, bar=c("none", "horizontal", "vertical"),
                   layout=TRUE, ...)
}

\arguments{

  \item{arrayCGH}{Object of class \code{\link{arrayCGH}}.}
  \item{variable}{Variable to be plotted}
  \item{Statistic}{Statistic to be plotted.}
  \item{Col}{Vector of columns coordinates.}
  \item{Row}{Vector of rows coordinates.}
  \item{ArrCol}{Number of columns for the blocs.}
  \item{ArrRow}{Number of rows for the blocs.}
  \item{SpotCol}{Number of column for each bloc.}
  \item{SpotRow}{Number of rows for each bloc.}
  \item{mediancenter}{If \code{mediancenter=TRUE}, values of \code{Statistic} are median-centered.}
  \item{col}{List of colors such as that generated by \code{Palettes}. In addition to these color palettes functions, a new function \code{\link{myPalette}} was defined to generate color palettes from user supplied low, middle, and high color values. }
  \item{contour}{If \code{contour=TRUE}, contour are plotted,
    otherwise they are not shown.}
  \item{nlevels}{Numbers of levels added by \code{contour} if \code{contour=TRUE}.}
  \item{zlim}{Numerical vector of length 2 giving the extreme values of
    \code{z} to associate with colors \code{low} and \code{high} of
    \code{\link{myPalette}}. By default \code{zlim} is the range of
    \code{z}.  Any values of \code{z} outside
    the interval \code{zlim} will be truncated to the relevant limit.}
  \item{bar}{If \code{bar=='horizontal'} (resp. \code{'vertical'}), an
    horizontal (resp. vertical) calibration color bar is shown to the
    right of the image.}
  \item{layout}{If \code{layout==TRUE} plot layout is automatically set
    when a color bar is asked for}
  \item{...}{Graphical parameters can be given as arguments to function
    \code{image}.}

  N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the
  values in 1:arrayCol*SpotCol

  }


\details{This function is very similar to the
  \code{maImage} written by Sandrine Dudoit
  (available in marrayPlots package) with
  added options \code{zlim}, \code{mediancenter} and \code{layout}.}

\value{An image is created on the current graphics device.}

\note{People interested in tools dealing with array CGH analysis can
  visit our web-page \url{http://bioinfo.curie.fr}.}

\author{Philippe Hupé, \email{glad@curie.fr}.}

\seealso{\code{image}, \code{contour}, \code{\link{arrayPersp}}, \code{\link{myPalette}}.}

\keyword{hplot}

\examples{
data(arrayCGH)

pdf(file="arrayCGH.pdf",height=21/cm(1),width=29.7/cm(1))
arrayPlot(array2$Log2Rat, array2$Col, array2$Row, 4,4,21,22, main="Spatial Image of array CGH")
dev.off()


# object of class arrayCGH

array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22))
class(array) <- "arrayCGH"

arrayPlot(array,"Log2Rat", main="Spatial Image of array CGH")

}