\HeaderA{plotSegmentationDots}{Plot points for a region along a chromosome}{plotSegmentationDots}
\keyword{hplot}{plotSegmentationDots}
\begin{Description}\relax
Plot points for a region along a chromosome
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSegmentationDots(dat, xlim, ylim, ylab, threshold=NA, 
                     chr=1, strand="+", vpr, colors, main, 
                     pointSize=unit(0.6, "mm"), showConfidenceIntervals=TRUE, 
                     sepPlots=FALSE, cexAxisLabel=1, cexAxis=1,...)
\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{ylim}] numeric vector containing the y limits of the plot.
\item[\code{ylab}] character scalar (if \code{sepPlots=FALSE}) or vector containing y-axis label(s).
\item[\code{threshold}] numeric scalar indicating the threshold of expression (default value is NA, for 
no threshold.  If a value is supplied, it is subtracted from the intensity measures in \code{dat\$y}.
\item[\code{chr}] integer of length 1 indicating the chromosome to be 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 the colors of data points and the 
last three to the colors of lines in the plot.
\item[\code{main}] character vector specifying plot title.
\item[\code{pointSize}] an object of class unit which specifies the size of each point.  Default value is \code{unit(0.6, "mm")}.
\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{sepPlots}] logical scalar indicating whether the intensities are plotted separately for each array (if \code{dat\$y} has multiple columns).  Defaults to FALSE, in which case the average intensity for each probe is plotted.  When TRUE, up to 3 arrays can be plotted separately (more than 3 gets crowded).
\item[\code{cexAxisLabel}] numeric scalar specifying the magnification to be used for the y-axis label relative to the current test size.
\item[\code{cexAxis}] numeric scalar specifying the magnification to be used for the y-axis annotation relative to the current text size.
\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{dots}.  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}

