\HeaderA{parallelCoordinates}{Parallel Coordinates}{parallelCoordinates}
\aliasA{parallel coordinates}{parallelCoordinates}{parallel coordinates}
\keyword{hplot}{parallelCoordinates}
\keyword{cluster}{parallelCoordinates}
\begin{Description}\relax
Represents expression levels through gene and/or condition profiles in
a bicluster as lines.
\end{Description}
\begin{Usage}
\begin{verbatim}
parallelCoordinates(x, bicResult, number,plotBoth=FALSE, plotcol=TRUE, compare=TRUE,info=F,bothlab=c("Rows","Columns"),ylab="Value",col=1,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The data matrix of the bicluster to be drawn
\item[\code{bicResult}] BiclustResult object with a bicluster result set
\item[\code{number}] Bicluster to be drawn from the result set 'bicResult'
\item[\code{plotBoth}] If 'TRUE', Parallel Coordinates of rows (Genes) and columns (Conditions) were drawn one below the other.
\item[\code{plotcol}] If 'TRUE', columns profiles are drawn, so each line represents one of the columns in the bicluster. Otherwise, row profiles are drawn. Default 'TRUE'
\item[\code{compare}] If 'TRUE',  values of the complete data matrix are considered and drawn as shaded lines. Default 'TRUE'
\item[\code{info}] If 'TRUE', a prepared Title is drawn
\item[\code{bothlab}] Names of the X-Axis if PlotBoth
\item[\code{ylab}] ylab
\item[\code{col}] col
\item[\code{...}] Plot Parameters
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Rodrigo Santamaria and Sebastian Kaiser
\email{rodri@usal.es}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{drawHeatmap}{drawHeatmap}} for alternative representation of biclusters and \code{\LinkA{bubbleplot}{bubbleplot}} for simultaneous representation of biclusters.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  #Random 100x50 matrix with a single, up-regulated 10x10 bicluster
  s2=matrix(rnorm(5000),100,50)
  s2[11:20,11:20]=rnorm(100,3,0.3)
  set.seed(1)
  bics <- biclust(s2,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
  iter.startup = 5, iter.layer = 30,  verbose = TRUE)
  parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=TRUE, plotcol=TRUE, compare=TRUE, info=TRUE,bothlab=c("Genes Bicluster 1","Conditions Bicluster 1"))
  parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=FALSE, plotcol=TRUE,  compare=FALSE, info=TRUE)
\end{ExampleCode}
\end{Examples}

