\HeaderA{maDefaultPar}{Default graphical parameters for microarray objects}{maDefaultPar}
\keyword{iplot}{maDefaultPar}
\keyword{dplot}{maDefaultPar}
\keyword{color}{maDefaultPar}
\begin{Description}\relax
This function returns default graphical parameters for microarray objects. The parameters may be passed as arguments to the functions \code{maBoxplot} and \code{maPlot}.
\end{Description}
\begin{Usage}
\begin{verbatim}
maDefaultPar(m, x, y, z)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{m}] Microarray object of class \code{"\LinkA{marrayRaw}{marrayRaw}"} and \code{"\LinkA{marrayNorm}{marrayNorm}"}.
\item[\code{x}] Name of accessor method for the abscissa spot statistic,
typically a slot name for the microarray object \code{m}, such as
\code{maA}.
\item[\code{y}] Name of accessor method for the ordinate spot statistic,
typically a slot name for the microarray object \code{m}, such as
\code{maM}.
\item[\code{z}] Name of accessor method for the spot statistic used to
stratify the data, typically a slot name for the microarray layout
object (see \code{"\LinkA{marrayLayout}{marrayLayout}"}) such as \code{maPlate} or
a method such as \code{maPrintTip}.
\end{ldescription}
\end{Arguments}
\begin{Value}
A list with elements
\begin{ldescription}
\item[\code{def.box}] default graphical parameters for \code{\LinkA{maBoxplot}{maBoxplot}}.
\item[\code{def.plot}] default graphical parameters for \code{\LinkA{maPlot}{maPlot}}.
\item[\code{def.lines}] default graphical parameters for functions such as \code{\LinkA{maLoessLines}{maLoessLines}} used in \code{\LinkA{maPlot}{maPlot}}.
\item[\code{def.legend}] default graphical parameters for functions such as \code{\LinkA{maLegendLines}{maLegendLines}} used in \code{\LinkA{maPlot}{maPlot}}.
\item[\code{def.text}] default graphical parameters for functions such as \code{\LinkA{maText}{maText}} used in \code{\LinkA{maPlot}{maPlot}}.
\end{ldescription}
\end{Value}
\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{maBoxplot}{maBoxplot}}, \code{\LinkA{maPlot}{maPlot}},
\code{\LinkA{maLegendLines}{maLegendLines}}, \code{\LinkA{maLoessLines}{maLoessLines}},
\code{\LinkA{maText}{maText}}, \code{\LinkA{maDotsDefaults}{maDotsDefaults}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# See examples for maPlot.

\end{ExampleCode}
\end{Examples}