\name{borderplot-methods}
\docType{methods}
\alias{borderplot-methods}
\alias{borderplot}
\title{Plots of Border Elements}
\description{
  Produce box-and-whisker plot(s) of the positive and negative feature intensities.

\emph{Usage}

\code{
borderplot(x,
           type    = c("pos", "neg"),
           qualopt = "raw",
           transfo = log2,
           range   = 0,
           names   = "namepart",
           ylim    = NULL,
           bmar    = NULL,
           las     = 2,
           ...)
}
}
\arguments{
  \item{x}{object of class \code{\link{QualTreeSet}}.}
  \item{type}{type of border elements to be used, one of \dQuote{pos}, \dQuote{neg}, or both.}
  \item{qualopt}{character string specifying whether to draw boxplots for \dQuote{raw},
  \dQuote{adjusted}, or \dQuote{normalized} border intensities.}
  \item{transfo}{a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.}
  \item{range}{determines how far the plot whiskers extend out from the box.}
  \item{names}{optional vector of sample names.}
  \item{ylim}{the y limits of the plot.}
  \item{bmar}{optional \code{list} for bottom margin and axis label magnification \code{cex.axis}.}
  \item{las}{the style of axis labels.}
  \item{\dots}{optional arguments to be passed to \code{borderplot}.}
}
\details{
 Creates a boxplot of the positive and negative feature intensities for an object of class
 \code{\link{QualTreeSet}}.

 For \code{names=NULL} full tree names will be displayed while for  \code{names="namepart"} tree
 names will be displayed without name extension. If \code{names} is a vector of tree names, only
 these columns will displayed as boxplot.

 For \code{bmar=NULL} the default list \code{bmar = list(b=6, cex.axis=1.0)} will be used initially.
 However, both bottom margin \code{b} and axis label magnification \code{cex.axis} will be adjusted
 depending on the number of label characters and the number of samples.  
}
\author{Christian Stratowa}
\seealso{\code{\link{coiplot}}, \code{\link{boxplot}}}
\examples{
\dontrun{
## border intensities, created by e.g. rmaPLM()
getTreeNames(rootFile(rlm.all), treetype="brd")
borderplot(rlm.all)
borderplot(rlm.all, type="pos")
borderplot(rlm.all, type="neg")
}
}
\keyword{methods}