\HeaderA{plotDensity}{Plot Densities}{plotDensity}
\methaliasA{plotDensity.AffyBatch}{plotDensity}{plotDensity.AffyBatch}
\keyword{hplot}{plotDensity}
\begin{Description}\relax
Plots the non-parametric density estimates using values contained in the
columns of a matrix.
\end{Description}
\begin{Usage}
\begin{verbatim}

plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6,
            na.rm = TRUE, ...)

plotDensity.AffyBatch(x, col = 1:6, log = TRUE,
                      which=c("pm","mm","both"),
                      ylab = "density",
                      xlab = NULL, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mat}] A matrix containing the values to make densities in the columns.
\item[\code{x}] A object of clase \code{\LinkA{AffyBatch}{AffyBatch}}
\item[\code{log}] logical value. If \code{TRUE} the log of the intensities in
the \code{AffyBatch} are plotted.
\item[\code{which}] should a histogram of the PMs, MMs, or both be made?
\item[\code{col}] The colors to use fot the different arrays
\item[\code{ylab}] a title for the y axis.
\item[\code{xlab}] a title for the x axis.
\item[\code{type}] type for the plot.
\item[\code{na.rm}] handling of \code{NA} values.
\item[\code{...}] graphical parameters can be given as arguments to \code{\LinkA{plot}{plot}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The list returned can be convenient for plotting large input matrices
with different colors/line types schemes
(the computation of the densities can take some time).

To match other functions in base R, this function should probably be
called \code{matdensity}, as it is sharing similarities with
\code{matplot} and \code{matlines}.
\end{Details}
\begin{Value}
It returns invisibly a list of two matrices `x' and `y'.
\end{Value}
\begin{Author}\relax
Ben Bolstad and Laurent Gautier
\end{Author}
\begin{Examples}
\begin{ExampleCode}
if (require(affydata)) {
  data(Dilution)
  plotDensity(exprs(Dilution), log="x")
}
\end{ExampleCode}
\end{Examples}

