dendrogram                package:mva                R Documentation

General Tree Structures

Description:

     Class `"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. Currently the code is in alpha stage and the API
     may change at any point in time.

Usage:

     plot(x, type=c("rectangle", "triangle"),
                     center=FALSE, xlab="", ylab="", ...)
     cut(x, h, ...)

Arguments:

       x: Object of class `"dendrogram"'.

    type: Type of plot.

  center: If `TRUE', nodes are plotted centered with respect to the
          leaves in the branch. Default is to plot them in the middle
          of all direct child nodes.

       h: Height at which the tree is cutted.

..., xlab, ylab: graphical parameters, or arguments for other methods.

Details:

     Warning: This documentation is preliminary.

     The dendrogram is directly represented as a nested list, where
     each list component corresponds to a branch of the tree. Hence,
     the first branch of tree `z' is `z[[1]]', the second branch of the
     corresponding subtree is `z[[1]][[2]]' etc.. Each node of the tree
     carries some information needed for efficient plotting or cutting
     as attributes:

     `members' number of leaves in the branch

     `height' Height at which the node is plotted

     `midpoint' Horizontal distance of the node from the left border of
          the branch

     `text' Text label of the node

     `edgetext' Text label for the edge leading to the node

     Terminal nodes (leaves of the tree) can have arbitrary value but
     must not be a list.

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

     Objects of class `"hclust"' can be converted to class
     `"dendrogram"' using method `as.dendrogram'.

     `plotNode()' and `plotNodeLimit()' are helper functions.

Examples:

     library(mva)
     data(USArrests)
     hc <- hclust(dist(USArrests), "ave")
     str(dend1 <- as.dendrogram(hc))
     plot(dend1)
     dend2 <- cut(dend1, h=70)
     plot(dend2$upper)
     plot(dend2$lower[[3]])

