\HeaderA{pmplot-methods}{Barplot of PM and MM Intensities.}{pmplot.Rdash.methods}
\aliasA{pmplot}{pmplot-methods}{pmplot}
\keyword{methods}{pmplot-methods}
\begin{Description}\relax
Creates a barplot of mean perfect match and mismatch intensities.

\emph{Usage}

\code{
pmplot(x, which = "", size = 0, transfo = NULL, method  = "mean", names = "namepart", beside = TRUE, col = c("red", "blue"), legend = c("PM","MM"), ...)
}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{DataTreeSet}{DataTreeSet}}.
\item[\code{which}] type of probes to be used, for details see \code{\LinkA{validData}{validData}}.
\item[\code{size}] length of sequence to be generated as subset.
\item[\code{transfo}] a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.
\item[\code{method}] method to compute average intensities, \dQuote{mean} or \dQuote{median}.
\item[\code{names}] optional vector of sample names.
\item[\code{beside}] logical. If \code{FALSE}, mean intensities are portrayed as stacked bars, 
and if \code{TRUE} the columns are portrayed as juxtaposed bars.
\item[\code{col}] color of PM, MM bars.
\item[\code{legend}] a vector of text used to construct a legend for the plot, 
or a logical indicating whether a legend should be included.
\item[\code{...}] optional arguments to be passed to \code{barplot}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Produces barplots of mean perfect match and mismatch intensities for slot \code{data}
for an object of class \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.

For \code{names=NULL} full column names of slot \code{data} will be displayed while for 
\code{names="namepart"} column names will be displayed without name extension. If \code{names}
is a vector of column names, only these columns will displayed as pmplot.
\end{Details}
\begin{Note}\relax
Data must first be attached to class \code{\LinkA{DataTreeSet}{DataTreeSet}} using method \code{\LinkA{attachInten}{attachInten}}.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{boxplot.dev}{boxplot.dev}}, \code{\LinkA{boxplot}{boxplot}}, \code{\LinkA{barplot}{barplot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
pmplot(data.test3)
}

## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)
\end{ExampleCode}
\end{Examples}

