\HeaderA{comparisonPlot}{Plot a vertical layout of panels for the comparison of different
along-chromosome profiles.}{comparisonPlot}
\keyword{manip}{comparisonPlot}
\begin{Description}\relax
This function is used for Figure 5 in the David et al. (PNAS 2006)
paper and in the Huber et al. methods paper.
\end{Description}
\begin{Usage}
\begin{verbatim}
comparisonPlot(x, y, xscale=range(x), yscale, anno, ticks, pch=20, cex=1, bgcol="#f2f2f2")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] numeric vector.
\item[\code{y}] list of numeric vector, each of same length as \code{x}.
\item[\code{xscale}] numeric vector of length 2.
\item[\code{yscale}] matrix with 2 rows and columns corresponding to the
elements of \code{x}.
\item[\code{anno}] dataframe with columns \code{start}, \code{end}, and
\code{name}, each row corresponds to one gene CDS to be plotted at the bottom.
\item[\code{ticks}] numeric vector, where to plot the ticks.
\item[\code{pch}] A numeric or character vector indicating what sort of
plotting symbol to use, see \code{\LinkA{grid.points}{grid.points}}.
\item[\code{cex}] Multiplier applied to fontsize, see \code{\LinkA{gpar}{gpar}}.
\item[\code{bgcol}] Color to use as background for some of the plot panels.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
Function is called for its side-effect.
\end{Value}
\begin{Author}\relax
W. Huber \email{huber@ebi.ac.uk}
\end{Author}
\begin{References}\relax
...
\end{References}
\begin{Examples}
\begin{ExampleCode}
  ##
\end{ExampleCode}
\end{Examples}

