\HeaderA{plot.mat}{Red and Green Color Image of Data Matrix}{plot.mat}
\keyword{hplot}{plot.mat}
\begin{Description}\relax
This function produces a red and green color image of a
data matrix using an RGB color specification. Larger entries are
represented with reds of increasing intensity, and smaller entries
are represented with greens of increasing intensity.
\end{Description}
\begin{Usage}
\begin{verbatim}
plot.mat(x, nrgcols=50, rlabels=FALSE, clabels=FALSE, rcols=1, ccols=1, title="",...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a matrix of numbers.
\item[\code{nrgcols}] the number of colors (>= 1) to be used in the red
and green palette.
\item[\code{rlabels}] vector of character strings to be placed at the row
tickpoints, labels for the rows of \code{X}.
\item[\code{clabels}] vector of character strings to be placed at the
column tickpoints, labels for the columns of \code{X}.
\item[\code{rcols}] colors to be used for the labels of the rows of
\code{X}. \code{rcols} can have either length 1, in which case
all the labels are displayed using the same color, or the same
length as \code{rlabels}, in which case a color is specified for the
label of each row of \code{X}.
\item[\code{ccols}] colors to be used for the labels of the columns of
\code{X}. \code{ccols} can have either length 1, in which case
all the labels are displayed using the same color, or the same
length as \code{clabels}, in which case a color is specified for the
label of each column of \code{X}.
\item[\code{title}] character string, overall title for the plot.
\item[\code{...}] graphical parameters may also be supplied as arguments  to
the function (see \code{\LinkA{par}{par}}).  E.g. \code{zlim=c(-3,3)}
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Sandrine Dudoit, \email{sandrine@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{plot.cor}{plot.cor}}, \code{\LinkA{rgcolors.func}{rgcolors.func}},
\code{\LinkA{cor.na}{cor.na}}, \code{\LinkA{cor}{cor}}, \code{\LinkA{image}{image}},
\code{\LinkA{rgb}{rgb}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(MouseArray)
##mouse.setup <- init.grid()
##mouse.data <- init.data() ## see \emph{init.data}
mouse.lratio <- stat.ma(mouse.data, mouse.setup)

## Looking at log ratios of mouse1
plot.mat(spatial.func(mouse.lratio$M[,1], mouse.setup))
\end{ExampleCode}
\end{Examples}

