\HeaderA{image}{Method image for objects defined in this package}{image}
\methaliasA{image.maiges}{image}{image.maiges}
\methaliasA{image.maigesActMod}{image}{image.maigesActMod}
\methaliasA{image.maigesActNet}{image}{image.maigesActNet}
\methaliasA{image.maigesANOVA}{image}{image.maigesANOVA}
\methaliasA{image.maigesRaw}{image}{image.maigesRaw}
\methaliasA{image.maigesRelNetB}{image}{image.maigesRelNetB}
\methaliasA{image.maigesRelNetM}{image}{image.maigesRelNetM}
\keyword{array}{image}
\begin{Description}\relax
Generic function \code{\LinkA{image}{image}} to display colour maps
of numerical values stored in objects defined in this package.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'maigesRaw':
image(x, ...)

## S3 method for class 'maiges':
image(x, ...)

## S3 method for class 'maigesANOVA':
image(x, ...)

## S3 method for class 'maigesRelNetB':
image(x=NULL, name=NULL, ...)

## S3 method for class 'maigesRelNetM':
image(x=NULL, names=NULL, ...)

## S3 method for class 'maigesActMod':
image(x, type=c("S","C")[2], keepEmpty=FALSE, ...)

## S3 method for class 'maigesActNet':
image(x, type=c("score","p-value")[1], ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object of class \code{\LinkA{maigesRaw}{maigesRaw}},
\code{\LinkA{maiges}{maiges}}, \code{\LinkA{maigesANOVA}{maigesANOVA}},
\code{\LinkA{maigesRelNetB}{maigesRelNetB}}, \code{\LinkA{maigesRelNetM}{maigesRelNetM}},
\code{\LinkA{maigesActMod}{maigesActMod}} or \code{\LinkA{maigesActNet}{maigesActNet}} defined in
this package.
\item[\code{name}] character string giving a name for sample type tested to
be plotted as a name in the method for class \code{\LinkA{maigesRelNetB}{maigesRelNetB}}.
\item[\code{names}] similar to the previous one, but it is a vector of length
3 for class \code{\LinkA{maigesRelNetM}{maigesRelNetM}}.
\item[\code{type}] string specifying the type of colour map to be plotted. For
class \code{\LinkA{maigesActMod}{maigesActMod}} it must be 'S' or 'C' for samples
or biological conditions, respectively. For class
\code{\LinkA{maigesActNet}{maigesActNet}} it must be 'score' or 'p-value' for the
statistics or p-values of the tests, respectively.
\item[\code{keepEmpty}] logical, if true the results of all gene groups are
displayed, else only the gene groups that present at least one
significant result are displayed.
\item[\code{...}] additional arguments for the generic method
\code{\LinkA{image}{image}} from \emph{graphics} package or
\code{\LinkA{maImage}{maImage}} defined in package \emph{marray} (for
\code{maigesRaw}, \code{maiges} or \code{maigesANOVA} classes), in
this case the additional parameters must not be named, because these
names conflict with the \code{boxplot} generic function definition.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This method uses the function \code{\LinkA{maImage}{maImage}} from
marray package to display colour maps of accessor methods defined into
\emph{marray} package for objects of class \code{\LinkA{maiges}{maiges}} or
\code{\LinkA{maigesRaw}{maigesRaw}} and \code{\LinkA{maigesANOVA}{maigesANOVA}}.

For objects of class
\code{\LinkA{maigesRelNetM}{maigesRelNetM}} the method displays 3 colour maps
representing the correlation values for the two groups tested and the
p-values of the tests.

For class \code{\LinkA{maigesRelNetB}{maigesRelNetB}} it
displays the correlation values for the type tested.

In objects of
class \code{\LinkA{maigesActMod}{maigesActMod}} it displays the fraction of genes
induced or repressed for each gene group, by samples or biological
type.

Finally, for class \code{\LinkA{maigesActNet}{maigesActNet}}, the method
display the matrix of statistics or p-values of the tests.

Pay attention, if you specify the parameter \emph{x} (but not named)
for \code{\LinkA{maImage}{maImage}}) it will plot the M values instead
of W (default).
\end{Details}
\begin{Author}\relax
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{image}{image}} in the \emph{graphics} package and
\code{\LinkA{maImage}{maImage}} in \emph{marray} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing image plots (using package marray), default method showing the
## W values (for 1st chip), after showing the A values (2nd chip) and
## red background (20th chip).
image(gastro.raw[,1])
image(gastro.raw[,2], "maA")
image(gastro.raw[,20], "maRb")

## Example for normalized objects (showing A values for the 5th chip).
image(gastro.norm[,5], "maA")


## Example for object of class maigesRelNetB

## Constructing the relevance network (Butte's method) for sample
## 'Tissue' equal to 'Neso' for the 1st gene group
gastro.net = relNetworkB(gastro.summ, sLabelID="Tissue", 
  samples="Neso", geneGrp=1, type="Rpearson")

image(gastro.net)



## Example for object of class maigesRelNetM

## Constructing the relevance network for sample
## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
  samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
  type="Rpearson")

image(gastro.net)
\end{ExampleCode}
\end{Examples}

