\HeaderA{identifyLines}{A function for identifying sample lines on an alongChrom()
plot.}{identifyLines}
\keyword{utilities}{identifyLines}
\begin{Description}\relax
Given an environment returned from alongChrom(), will call identify()
on the alongChrom() plot.
\end{Description}
\begin{Usage}
\begin{verbatim}
identifyLines(identEnvir,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{identEnvir}] An environment created by alongChrom.
\item[\code{...}] Any extra arguments are passed on to identify().
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The environment contains two vectors of points - "X" and "Y" are their
labels, and contain the X and Y points respectively.  These vectors
are extracted out of the environment and fed into an identify() call
(with some extra processing to get the labeling correct.)  As with
identify(), one need only to right click to exit from the function.
\end{Details}
\begin{Author}\relax
Jeff Gentry
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{alongChrom}{alongChrom}}, \code{\LinkA{identify}{identify}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
   data(sample.exprSet)

   ## 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")
     lty <- c(1, 2, 3, 4, 5)
     cols <- c("red", "green", "blue", "orange", "magenta", "black")
     identEnv <- alongChrom(sample.exprSet,"1", z, xloc="equispaced",
                          plotFormat="cumulative", scale="none",
                          lty,cols)
     if (interactive()) {
       identifyLines(identEnv)
     }
  } else print("This example needs the hgu95av2 data package")
\end{ExampleCode}
\end{Examples}

