\name{plotCombination2genes}
\alias{plotCombination2genes}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Plot a Combination of Two Genes}
\description{
  Plot a Combination of Two Genes
}
\usage{
plotCombination2genes(probesetId1 = NULL, probesetId2 = NULL, geneSymbol1 = NULL,
 geneSymbol2 = NULL, object, groups, addLegend = TRUE, legendPos = "topleft", probe2gene = TRUE, colvec = NULL, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{probesetId1}{First probeset id, plotted in the x-axis}
  \item{probesetId2}{Second probeset id, plotted in the y-axis}
  \item{geneSymbol1}{First gene symbol, plotted in the x-axis}
  \item{geneSymbol2}{Second gene symbol, plotted in the y-axis}
  \item{object}{ExpressionSet object for the experiment}
  \item{groups}{string containing the name of the grouping variable}
  \item{addLegend}{Logical value to indicate whether a legend needs to be drawn.}
  \item{legendPos}{Position on the graph where to put the legend}
  \item{probe2gene}{should the probeset be translated to a gene symbol
    (used for the default title of the plot)}
  \item{colvec}{a character vector of colors. If not specified it will be 
  			automatically generated by \code{a4palette}}
  \item{\dots}{This allows to specify typical arguments in the \code{plot} function}
}
\value{
  If a gene id is given, the plots for only the first probeset is displayed 
  and a character vector of corresponding probeset IDs is returned invisibly. 
  
  It is a list containing
  \item{probeset1 }{Probeset ids measuring 'gene1'}
  \item{probeset1 }{Probeset ids measuring 'gene1'}

  If a probeset id is given, one single profile plot for the probeset is 
  displayed.
  }
\author{W. Talloen, T. Verbeke}
\seealso{\code{\link{plot1gene}}}

\examples{
if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)

  aa <- plotCombination2genes(geneSymbol1 = 'HLA-DPB1', geneSymbol2 = 'CD3D',
			object = ALL, groups = "BT",
			addLegend = TRUE, legendPos = 'topright')
  aa
}
}
\keyword{dplot}