\HeaderA{drawHeatmap}{Draw Heatmap}{drawHeatmap}
\aliasA{drawHeatmap2}{drawHeatmap}{drawHeatmap2}
\aliasA{heatmap}{drawHeatmap}{heatmap}
\keyword{hplot}{drawHeatmap}
\keyword{cluster}{drawHeatmap}
\begin{Description}\relax
Draws a microarray data matrix as a heatmap, with rows and colums
reordered so the rows and columns of the input bicluster will be at top-left
of the matrix.
\end{Description}
\begin{Usage}
\begin{verbatim}
drawHeatmap(x,bicResult=NULL,number=NA,local=TRUE, beamercolor=FALSE,paleta,...)
drawHeatmap2(x,bicResult=NULL,number=NA,plotAll=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The data matrix where the bicluster is to be drawn.
\item[\code{bicResult}] BiclustResult object with a bicluster result set. If this value
is set to NULL, the data matrix is drawn as a heatmap, without any reordering. Default NULL.
\item[\code{number}] Bicluster to be drawn from the result set 'bicResult'. If bicResult is set to
NULL, this value is ignored. Default NA
\item[\code{local}] If TRUE, only rows and columns of the bicluster were drawn.
\item[\code{plotAll}] If TRUE, all Bicluster of result set 'bicResult' were drawn.
\item[\code{beamercolor}] If TRUE, palete colors are used.
\item[\code{paleta}] Colors
\item[\code{...}] Additional plot options
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
'plotAll' only works if there is a exclusive rows and column Result!
\end{Details}
\begin{Author}\relax
Rodrigo Santamaria \email{rodri@usal.es},
Sebastian Kaiser
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{bubbleplot}{bubbleplot}} for simultaneous representation of biclusters.\bsl{}
\code{\LinkA{parallelCoordinates}{parallelCoordinates}}for single representation of biclusters as lines of gene or condition profiles.
\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)
  drawHeatmap(s2,bics,1)

\end{ExampleCode}
\end{Examples}

