\HeaderA{boxplot}{Method boxplot for objects defined in this package}{boxplot}
\methaliasA{boxplot.maiges}{boxplot}{boxplot.maiges}
\methaliasA{boxplot.maigesANOVA}{boxplot}{boxplot.maigesANOVA}
\methaliasA{boxplot.maigesDEcluster}{boxplot}{boxplot.maigesDEcluster}
\methaliasA{boxplot.maigesRaw}{boxplot}{boxplot.maigesRaw}
\keyword{array}{boxplot}
\begin{Description}\relax
Generic function \code{\LinkA{boxplot}{boxplot}} to display boxplots
of the data.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'maigesRaw':
boxplot(x, ...)

## S3 method for class 'maiges':
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

## S3 method for class 'maigesANOVA':
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

## S3 method for class 'maigesDEcluster':
boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object of any class defined in this package
\item[\code{name}] character string specifying a gene to do boxplot of their
expression values along the types specified by \code{sLabelID}.
\item[\code{gLabelID}] character value giving the name of gene label to be
used to search for parameter \code{name}.
\item[\code{sLabelID}] idem to \code{gLabelID}, specifying the name of sample
label to be used to separate the gene observations.
\item[\code{gSamples}] a named list containing character vectors defining
groups of samples from \code{sLabelID}.
\item[\code{...}] additional parameters to \code{\LinkA{boxplot}{boxplot}}
method defined in \emph{graphics} package or to
\code{\LinkA{maBoxplot}{maBoxplot}} method defined in \emph{marray}
package (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{maBoxplot}{maBoxplot}} from
marray package to show boxplots of the W values along all the slides of a
dataset or along specific accessor methods to stratify the data in
objects of class \code{\LinkA{maigesRaw}{maigesRaw}}. For objects of classes
\code{\LinkA{maiges}{maiges}} or \code{\LinkA{maigesANOVA}{maigesANOVA}} this is also done if
the argument \code{name} is NULL, else the method shows boxplots for
the expression values of the gene specified by \code{name} stratified by
sample types from \code{sLabelID}. For objects of class
\code{\LinkA{maigesDEcluster}{maigesDEcluster}} only boxplots of genes are produced and
the argument \code{name} may not be NULL.

If you especify the \code{y} parameter (but not named), defined for
the method \code{\LinkA{maBoxplot}{maBoxplot}} in package \emph{marray},
it will be displayed the M values instead of W.
\end{Details}
\begin{Author}\relax
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{maBoxplot}{maBoxplot}} in the \emph{marray} package and
\code{\LinkA{boxplot}{boxplot}} in the \emph{graphics} package.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## To see the boxplots for W values in all chips
boxplot(gastro.raw)  ## maigesRaw class
boxplot(gastro.norm) ## maigesNorm class
boxplot(gastro.summ) ## summarized data (also maigesNorm class)

## To see the boxplots for W values in individual chips
## separating into print tips.
boxplot(gastro.raw[,1])  ## maigesRaw class, first chip
boxplot(gastro.norm[,8]) ## maigesNorm class, 8th chip
boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class), 19th chip

## Boxplot for individual genes into ANOVA model fitting
gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")
gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)

boxplot(gastro.ANOVAfit, name="KLK13", gLabelID="GeneName", 
sLabelID="Tissue")
\end{ExampleCode}
\end{Examples}

