\name{probesetplot-methods}
\docType{methods}
\alias{probesetplot-methods}
\alias{probesetplot}
\title{Plot of Probe Intensities for a Probeset.}
\description{
Creates a line plot of probe intensities for a probeset.

\emph{Usage}

\code{
probesetplot(x,
             unitID,
             unittype   = "transcript",
             which      = "pm",
             transfo    = log2,
             names      = "namepart",
             ylim       = NULL,
             col        = 1:6,
             lty        = 1:5,
             add.legend = FALSE,
            ...) 
}
}
\arguments{
  \item{x}{object of class \code{\link{DataTreeSet}}.}
  \item{unitID}{unit ID of probeset with type of ID determined by parameter \code{unittype}.}
  \item{unittype}{\code{character} vector, one of \dQuote{unit}, \dQuote{transcript}, \dQuote{probeset}.}
  \item{which}{type of probes to be used, for details see \code{\link{validData}}.}
  \item{transfo}{a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.}
  \item{names}{optional vector of sample names.}
  \item{ylim}{range for the plotted y values.}
  \item{col}{color to use for the different samples.}
  \item{lty}{line types to use for the different samples.}
  \item{add.legend}{logical, if TRUE a legend of sample names will be drawn. Optionally, a character
   indicating the position of the legend, default is \dQuote{topleft}.}
  \item{\dots}{optional arguments to be passed to \code{probesetplot}.}
}
\details{
 Produces line plots of the probe intensities for probeset \code{unitID}. Probe intensities are 
 taken from slot \code{data}. 

 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, line plots of probe intensities will only be drawn for these columns.
}
\author{Christian Stratowa}
\note{
 Data must first be attached to class \code{\link{DataTreeSet}} using method \code{\link{attachInten}}.
 Furthermore, unit names must be attached using method \code{\link{attachUnitNames}}.
}
\seealso{\code{\link{plotPM}}, \code{\link{boxplot}}, \code{\link{barplot}}}
\examples{
## 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 probe intensities and optionally unit names
data.test3 <- attachUnitNames(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
probesetplot(data.test3, unitID="100084_at", unittype="transcript", add.legend=TRUE)
}

## optionally remove unit names and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeUnitNames(data.test3)
}
\keyword{methods}