\HeaderA{cColor}{A function for marking specific probes on a cPlot.}{cColor}
\keyword{utilities}{cColor}
\begin{Description}\relax
Given a set of probes, will highlight them in the color desired on
a plot which has already been created via the function cPlot().
\end{Description}
\begin{Usage}
\begin{verbatim}
cColor(probes, color, plotChroms, scale=c("relative","max"), glen=0.4)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{probes}] The probes that are being highlighted.
\item[\code{color}] The color to highlight the probes.
\item[\code{plotChroms}] An object of type \code{chromLocation} which contains all
the gene information to be plotted.
\item[\code{scale}] Whether to plot the graph scaled absolutely or relative
by chromosome.  Default is absolute.
\item[\code{glen}] The length of the gene line plotted.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
It is important to call the function \code{cPlot()} first.  This function
will then search for the specific locations of the probes desired,
which are contained within the \code{plotChroms} instance of a
\code{chromLocation} class.  It will then pass these on to the
plotting routine to highlight the desired locations.  NOTE:  It
is important that \code{plotChroms}, \code{scale} and \code{glen}
parameters are the same as used for \code{cPlot()}.
\end{Details}
\begin{Author}\relax
Jeff Gentry
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{cPlot}{cPlot}}, \code{\LinkA{chromLocation-class}{chromLocation.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  if(match("hgu95av2.db", .packages(all = TRUE), nomatch=0)) {
    library("hgu95av2.db")
    z <- buildChromLocation("hgu95av2")
    cPlot(z)
    probes <- c("266_s_at", "31411_at", "610_at", "failExample")
    cColor(probes, "red", z)
    probes2 <- c("960_g_at", "41807_at", "931_at", "39032_at")
    cColor(probes2, "blue", z)
  } else
    print("Need hgu95av2.db data package for the example")
  \end{ExampleCode}
\end{Examples}

