dendrogram               package:stats               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.

     The code is still in testing stage and the API may change in the
     future.

Usage:

     as.dendrogram(object, ...)
     ## S3 method for class 'hclust':
     as.dendrogram(object, hang = -1, ...)

     ## S3 method for class 'dendrogram':
     plot(x, type = c("rectangle", "triangle"),
           center = FALSE,
           edge.root = is.leaf(x) || !is.null(attr(x,"edgetext")),
           nodePar = NULL, edgePar = list(),
           leaflab = c("perpendicular", "textlike", "none"),
           dLeaf = NULL, xlab = "", ylab = "", xaxt = "n", yaxt = "s",
           horiz = FALSE, frame.plot = FALSE, xlim, ylim, ...)

     ## S3 method for class 'dendrogram':
     cut(x, h, ...)

     ## S3 method for class 'dendrogram':
     print(x, digits, ...)

     ## S3 method for class 'dendrogram':
     rev(x)

     ## S3 method for class 'dendrogram':
     str(object, max.level = NA, digits.d = 3,
         give.attr = FALSE, wid = getOption("width"),
         nest.lev = 0, indent.str = "", stem = "--", ...)

     is.leaf(object)

Arguments:

  object: any R object that can be made into one of class
          '"dendrogram"'.

       x: object of class '"dendrogram"'.

    hang: numeric scalar indicating how the _height_ of leaves should
          be computed from the heights of their parents; see
          'plot.hclust'.

    type: type of plot.

  center: logical; if '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.

edge.root: logical; if true, draw an edge to the root node.

 nodePar: a 'list' of plotting parameters to use for the nodes (see
          'points') or 'NULL' by default which does not draw symbols at
          the nodes.  The list may contain components named 'pch',
          'cex', 'col', and/or 'bg' each of which can have length two
          for specifying separate attributes for _inner_ nodes and
          _leaves_.

 edgePar: a 'list' of plotting parameters to use for the edge
          'segments' and labels (if there's an 'edgetext').  The list
          may contain components named 'col', 'lty' and 'lwd' (for the
          segments), 'p.col', 'p.lwd', and 'p.lty' (for the 'polygon'
          around the text) and 't.col' for the text color.  As with
          'nodePar', each can have length two for differentiating
          leaves and inner nodes. 

 leaflab: a string specifying how leaves are labeled.  The default
          '"perpendicular"' write text vertically (by default).
           '"textlike"' writes text horizontally (in a rectangle), and 
           '"none"' suppresses leaf labels.

   dLeaf: a number specifying the *d*istance in user coordinates
          between the tip of a leaf and its label.  If 'NULL' as per
          default, 3/4 of a letter width or height is used.

   horiz: logical indicating if the dendrogram should be drawn
          _horizontally_ or not.

frame.plot: logical indicating if a box around the plot should be
          drawn, see 'plot.default'.

       h: height at which the tree is cut.

xlim, ylim: optional x- and y-limits of the plot, passed to
          'plot.default'.  The defaults for these show the full
          dendrogram.

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

  digits: integer specifying the precision for printing, see
          'print.default'.

max.level, digits.d, give.attr, wid, nest.lev, indent.str: arguments to
          'str', see 'str.default()'.  Note that 'give.attr = FALSE'
          still shows 'height' and 'members' attributes for each node.

    stem: a string used for 'str()' specifying the _stem_ to use for
          each dendrogram branch.

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 '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, of which only 'members', 'height' and 'leaf' for
     leaves are compulsory:

     'members' total number of leaves in the branch

     'height' numeric non-negative height at which the node is plotted.

     '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 'plot(*, center=FALSE)'.

     'label' character; the label of the node

     'x.member' for 'cut()$upper', the number of _former_ members; more
          generally a substitute for the 'members' component used for
          'horizontal' (when 'horiz = FALSE', else 'vertical')
          alignment.

     'edgetext' character; the label for the edge leading to the node

     'nodePar' a named list (of length-1 components) specifying
          node-specific attributes for 'points' plotting, see the
          'nodePar' argument above.

     'edgePar' a named list (of length-1 components) specifying
          attributes for 'segments' plotting of the edge leading to the
          node, and drawing of the 'edgetext' if available, see the
          'edgePar' argument above.

     'leaf' logical, if 'TRUE', the node is a leaf of the tree.

     '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'.

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

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

     'rev.dendrogram' simply returns the dendrogram 'x' with reversed
     nodes, see also 'reorder.dendrogram'.

     'is.leaf(object)' is logical indicating if 'object' is a leaf (the
     most simple dendrogram). 'plotNode()' and 'plotNodeLimit()' are
     helper functions.

Warning:

     Some operations on dendrograms (including plotting) make use of
     recursion.  For very deep trees It may be necessary to increase
     'options("expressions")': if you do you are likely to need to set
     the C stack size larger than the OS default if possible (which it
     is not on Windows).

Note:

     When using 'type = "triangle"', 'center = TRUE' often looks
     better.

See Also:

     'order.dendrogram' also on the 'labels' method for dendrograms.

Examples:

     require(graphics); require(utils)

     hc <- hclust(dist(USArrests), "ave")
     (dend1 <- as.dendrogram(hc)) # "print()" method
     str(dend1)          # "str()" method
     str(dend1, max = 2) # only the first two sub-levels

     op <- par(mfrow= c(2,2), mar = c(5,2,1,4))
     plot(dend1)
     ## "triangle" type and show inner nodes:
     plot(dend1, nodePar=list(pch = c(1,NA), cex=0.8, lab.cex = 0.8),
           type = "t", center=TRUE)
     plot(dend1, edgePar=list(col = 1:2, lty = 2:3),
          dLeaf=1, 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$upper)
     ## leafs are wrong horizontally:
     plot(dend2$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$lower[[2]], nodePar=list(col=1),# non empty list
          edgePar = list(lty=1:2, col=2:1), edge.root=TRUE)
     par(op)
     str(d3 <- dend2$lower[[2]][[2]][[1]])

     ## "Zoom" in to the first dendrogram :
     plot(dend1, xlim = c(1,20), ylim = c(1,50))

     nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22,
                bg= c("light blue", "pink"),
                lab.cex = 0.75, lab.col = "tomato")
     plot(d3, nodePar= nP, edgePar = list(col="gray", lwd=2), horiz = TRUE)
     addE <- function(n) {
           if(!is.leaf(n)) {
             attr(n, "edgePar") <- list(p.col="plum")
             attr(n, "edgetext") <- paste(attr(n,"members"),"members")
           }
           n
     }
     d3e <- dendrapply(d3, addE)
     plot(d3e, nodePar= nP)
     plot(d3e, nodePar= nP, leaflab = "textlike")

