\HeaderA{plotSegmentationHeatmap}{Plot a heatmap diagram for a region along a chromosome}{plotSegmentationHeatmap}
\keyword{hplot}{plotSegmentationHeatmap}
\begin{Description}\relax
Plot a heatmap diagram for a region along a chromosome
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSegmentationHeatmap(dat, xlim, ylab, rowNames, 
                        chr=1, strand="+", vpr, colors,                 
                        colHeatmap=colorRamp(brewer.pal(9, "YlGnBu")), 
                        showConfidenceIntervals=TRUE, main, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{dat}] list containing data to be plotted (see \emph{Details} section below for particulars).
\item[\code{xlim}] integer vector of length 2 with start and end coordinates (in bases) for plotting.
\item[\code{ylab}] character scalar specifying y-axis label.
\item[\code{rowNames}] character vector specifying a name for each row in the heatmap plot.
\item[\code{chr}] integer of length 1 indicating the chromosome to plot (defaults to 1).
\item[\code{strand}] character scalar which should be set to either \code{+} or \code{-} to 
indicate which strand of DNA to plot the intensity values from (defaults to "+").
\item[\code{vpr}] which viewport to plot the figure in.  If this function is called directly 
by the user this argument should be left missing.
\item[\code{colors}] named character vector, optional. If missing, 
a default color scheme is used:
\code{c("+"="\#00441b", "-"="\#081d58", "duplicated"="grey", "cp"="\#101010", 
   "highlight"="red", "threshold"="grey")}, 
where the first three elements refer to colors of data points and the 
last three to those of lines in the plot.
\item[\code{colHeatmap}] function describing color scheme for the heatmap plot (defaults to
\code{YlGnBu} from RColorBrewer package).
\item[\code{showConfidenceIntervals}] logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).
\item[\code{main}] character vector specifying plot title.
\item[\code{...}] additional arguments.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is called by \code{plotAlongChrom} when the argument \code{what} is set to \code{heatmap}.  Although this function can be called directly by the user, this is not recommended.
The \code{dat} list contains the following items:
items \code{x}: x-coordinates (in bases) along chromosome, 
\Enumerate{
\item \code{y}: intensity matrix of probes along chromosome,
\item \code{flag}: indicates probe uniqueness in the genome.  Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.
\item \code{extras}: (optional) matrix of additional values (such as test-statistics/p-values) to be plotted.
}
\end{Details}
\begin{Author}\relax
Wolfgang Huber <huber@ebi.ac.uk>
\end{Author}
\begin{Examples}
\begin{ExampleCode}\end{ExampleCode}
\end{Examples}

