\name{dendrogram}
\title{General Tree Structures}
\alias{dendrogram}% the class
\alias{as.dendrogram}
\alias{as.dendrogram.hclust}
\alias{cut.dendrogram}
\alias{[[.dendrogram}
\alias{print.dendrogram}
\alias{rev.dendrogram}
\alias{str.dendrogram}
\alias{plot.dendrogram}
%\alias{plotNode}
%\alias{plotNodeLimit}
%\alias{isLeaf}
\description{
  Class \code{"dendrogram"} provides general functions for handling
  tree-like structures.  It is intended as a replacement for similar
  functions in hierarchical clustering and classification/regression
  trees, such that all of these can use the same engine for plotting or
  cutting trees.

  The code is still in testing stage and the API may
  change in the future.
}
\usage{
as.dendrogram(object, \dots)
\method{as.dendrogram}{hclust}(object, hang = -1, \dots)

\method{plot}{dendrogram}(x, type = c("rectangle", "triangle"),
      center = FALSE, edge.root = isLeaf(x) || !is.null(attr(x,"edgetext")),
      nodePar = NULL, edgePar = list(), xlab = "", ylab = "",
      horiz = FALSE, frame.plot = FALSE, \dots)

\method{cut}{dendrogram}(x, h, \dots)

\method{print}{dendrogram}(x, digits, \dots)

\method{rev}{dendrogram}(x)

\method{str}{dendrogram}(object, max.level = 0, digits.d = 3,
    give.attr = FALSE, wid = getOption("width"),
    nest.lev = 0, indent.str = "", \dots)
}
\arguments{
  \item{object}{any \R object that can be made into one of class
    \code{"dendrogram"}.}
  \item{x}{object of class \code{"dendrogram"}.}
  \item{hang}{numeric scalar indicating how the \emph{height} of leaves
    should be computed from the heights of their parents; see
    \code{\link{plot.hclust}}.}
  \item{type}{type of plot.}
  \item{center}{logical; if \code{TRUE}, nodes are plotted centered with
    respect to the leaves in the branch.  Otherwise (default), plot them
    in the middle of all direct child nodes.}
  \item{edge.root}{logical; if true, draw an edge to the root node.}
  \item{nodePar}{a \code{list} of plotting parameters to use for the
    nodes (see \code{\link{points}}) or \code{NULL} by default which
    does not draw symbols at the nodes.  The list may contain components
    named \code{pch}, \code{cex}, \code{col}, and/or \code{bg} each of
    which can have length two for specifying separate attributes for
    \emph{inner} nodes and \emph{leaves}.}
  \item{edgePar}{a \code{list} of plotting parameters to use for the
    edge (see \code{\link{lines}}).  The list may contain components
    named \code{col}, \code{lty} and/or \code{lwd}.}
  \item{horiz}{logical indicating if the dendrogram should be draw
    \emph{horizontally} or not.}
  \item{frame.plot}{logical indicating if a box around the plot should
    be drawn, see \code{\link{plot.default}}.}
  \item{h}{height at which the tree is cut.}
  \item{\dots, xlab, ylab}{graphical parameters, or arguments for
    other methods.}
  \item{digits}{integer specifiying the precision for printing, see
    \code{\link{print.default}}.}
  \item{max.level, digits.d, give.attr, wid, nest.lev, indent.str}{%
    arguments to \code{str}, see \code{\link{str.default}()}.  Note that
    by default \code{give.attr = FALSE}, it still shows \code{height}
    and \code{members} attributes for each node.}
}
\details{
  Warning: This documentation is preliminary.

  The dendrogram is directly represented as a nested list where each
  component corresponds to a branch of the tree.  Hence, the first
  branch of tree \code{z} is \code{z[[1]]}, the second branch of the
  corresponding subtree is \code{z[[1]][[2]]} etc.. Each node of the tree
  carries some information needed for efficient plotting or cutting as
  attributes:
  \describe{
    \item{\code{members}}{total number of leaves in the branch}
    \item{\code{height}}{numeric non-negative height at which the node
      is plotted.}
    \item{\code{midpoint}}{numeric horizontal distance of the node from
      the left border (the leftmost leaf) of the branch (unit 1 between
      all leaves).  This is used for \code{plot(*, center=FALSE)}.}
    \item{\code{label}}{character; the label of the node}
    \item{\code{edgetext}}{character; the label for the edge leading to
      the node}
    \item{\code{nodePar}}{a named list of length one vectors specifying
      node-specific attributes for \code{\link{points}} plotting, see
      the \code{nodePar} argument above.}
    \item{\code{edgePar}}{a named list of length one vectors specifying
      attributes for \code{\link{segments}} plotting of the edge leading
      to the node, see the \code{edgePar} argument above.}
    \item{\code{leaf}}{logical, if \code{TRUE}, the node is a leaf of
      the tree.}%  This will often be a \code{\link{character}} which can
    %      be used for plotting instead of the \code{text} attribute.}
  }

  \code{cut.dendrogram()} returns a list with components \code{$upper}
  and \code{$lower}, the first is a truncated version of the original
  tree, also of class \code{dendrogram}, the latter a list with the
  branches obtained from cutting the tree, each a \code{dendrogram}.

  There are \code{\link{[[}}, \code{\link{print}}, and \code{\link{str}}
  methods for \code{"dendrogram"} objects where the first one
  (extraction) ensures that selecting sub-branches keeps the class.

  Objects of class \code{"hclust"} can be converted to class
  \code{"dendrogram"} using method \code{as.dendrogram}.

  \code{isLeaf()}, \code{plotNode()} and \code{plotNodeLimit()} are helper
  functions.
}
\note{
  When using \code{type = "triangle"}, \code{center = TRUE} often looks
  better.
}
\examples{
data(USArrests)
hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc)) # "print()" method
str(dend1) # "str()" method

op <- par(mfrow= c(2,2), mar = c(3,3,1,1))
plot(dend1)
## "triangle" type and show inner nodes:
plot(dend1, nodePar=list(pch = c(1,NA),cex=0.8), type = "t", center=TRUE)
plot(dend1, edgePar=list(col = 1:2, lty = 2:3), edge.root = TRUE)
plot(dend1, nodePar=list(pch = 2:1,cex=.4*2:1, col = 2:3), horiz = TRUE)

dend2 <- cut(dend1, h=70)
plot(dend2$upper)
## leafs are wrong horizontally:%% FIXME ?!?
plot(dend2$upper, nodePar=list(pch = c(1,7), col = 2:1))
##  dend2$lower is *NOT* a dendrogram, but a list of .. :
plot(dend2$lower[[3]], nodePar=list(col=4), horiz = TRUE, type = "tr")
## "inner" and "leaf" edges in different type & color :
plot(dend2$lower[[2]], nodePar=list(col=1),# non empty list
     edgePar = list(lty=1:2, col=2:1), edge.root=TRUE)
par(op)
}
\keyword{multivariate}
\keyword{tree}% FIXME: want as.dendrogram.tree() etc!
\keyword{hplot}% only for plot.()
