\HeaderA{maImage.func}{Color image for cDNA microarray spot statistics}{maImage.func}
\keyword{hplot}{maImage.func}
\begin{Description}\relax
This function 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 M, 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. This function is called by \code{\LinkA{maImage}{maImage}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
maImage.func(x, L, subset=TRUE, col=heat.colors(12), contours=FALSE, overlay=NULL, ol.col=1,  ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A "numeric" vector of spot statistics.
\item[\code{L}] An object of class \code{"\LinkA{marrayLayout}{marrayLayout}"}, if L is
missing we will assume the dimension of x.
\item[\code{subset}] A "logical" or "numeric" vector indicating the subset of spots to display on the image.
\item[\code{col}] A list of colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors, or similar functions. In addition to these color palette functions, a new function  \code{\LinkA{maPalette}{maPalette}} was defined to generate color palettes from user supplied low, middle, and high color values.
\item[\code{contours}] If \code{contours=TRUE}, contours are plotted,
otherwise they are not shown.
\item[\code{overlay}] A logical vector of spots to be highlighted on the image plots.
\item[\code{ol.col}] Color of the overlay spots.
\item[\code{...}] Optional graphical parameters, see \code{\LinkA{par}{par}}.
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Sandrine Dudoit, \url{http://www.stat.berkeley.edu/~sandrine}.
\end{Author}
\begin{References}\relax
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, \emph{The Analysis of Gene Expression Data: Methods and Software}, Springer, New York.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{image}{image}}, \code{\LinkA{maImage}{maImage}}, \code{\LinkA{maColorBar}{maColorBar}}, \code{\LinkA{maPalette}{maPalette}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# See examples for image.
\end{ExampleCode}
\end{Examples}