+\name{trex}
+\alias{trex}
+\title{Tree Explorer With Multiple Devices}
+\description{
+ This functions requires a plotted tree: the user is invited to click
+ close to a node and the corresponding subtree (or clade) is plotted on
+ a new window.
+}
+\usage{
+trex(phy, title = TRUE, subbg = "lightyellow3",
+ return.tree = FALSE, ...)
+}
+\arguments{
+ \item{phy}{an object of class \code{"phylo"}.}
+ \item{title}{a logical or a character string (see details).}
+ \item{subbg}{a character string giving the background colour for the
+ subtree.}
+ \item{return.tree}{a logical: if \code{TRUE}, the subtree is returned
+ after being plotted and the operation is stopped.}
+ \item{\dots}{further arguments to pass to \code{plot.phylo}.}
+}
+\details{
+ This function works with a tree (freshly) plotted on an interactive
+ graphical device (i.e., not a file). After calling \code{trex}, the
+ user clicks close to a node of the tree, then the clade from this node
+ is plotted on a \emph{new} window. The user can click as many times on
+ the main tree: the clades are plotted successively on the \emph{same}
+ new window. The process is stopped by a right-click. If the user clicks
+ too close to the tips, a message ``Try again!'' is printed.
+
+ Each time \code{trex} is called, the subtree is plotted on a new
+ window without closing or deleting those possibly already
+ plotted. They may be distinguished with the options \code{title}
+ and/or \code{subbg}.
+
+ In all cases, the device where \code{phy} is plotted is the active
+ window after the operation. It should \emph{not} be closed during the
+ whole process.
+
+ If \code{title = TRUE}, a default title is printed on the new window
+ using the node label, or the node number if there are no node labels
+ in the tree. If \code{title = FALSE}, no title is printed. If
+ \code{title} is a character string, this is used for the title.
+}
+\value{
+ an object of class \code{"phylo"} if \code{return.tree = TRUE}
+}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link{plot.phylo}}, \code{\link{identify.phylo}}
+}
+\examples{
+\dontrun{
+tr <- rcoal(1000)
+plot(tr, show.tip.label = FALSE)
+trex(tr) # left-click as many times as you want, then right-click
+tr <- makeNodeLabel(tr)
+trex(tr, subbg = "lightgreen") # id.
+
+## generate a random colour with control on the darkness:
+rRGB <- function(a, b)
+ rgb(runif(1, a, b), runif(1, a, b), runif(1, a, b))
+
+### with a random pale background:
+trex(tr, subbg = rRGB(0.8, 1))
+## the above can be called many times...
+graphics.off() # close all graphical devices
+}}
+\keyword{hplot}