\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}
   ## A bit of a hack to not have a package dependency on hgu95av2
   ## but need to fiddle w/ the warn level to not fail the example anyways.
   curWarn <- options(warn=0)
   on.exit(options(warn=curWarn), add=TRUE)
   if (require(hgu95av2)) {

     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 data package to run example")
\end{ExampleCode}
\end{Examples}

