dendrogram {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'
as.hclust(x, ...)

## 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'
merge(x, y, ..., height)

## 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 = "", last.str = "`", stem = "--",
    ...)

is.leaf(object)

Arguments

object any R object that can be made into one of class "dendrogram".
x,y object(s) 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, xpd, and/or bg each of which can have length two for specifying separate attributes for inner nodes and leaves. Note that the default of pch is 1:2, so you may want to use pch = NA if you specify nodePar.
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 distance 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.
height height at which the two dendrogram should be merged. If not specified (or NULL), the default is ten percent larger than the (larger of the) two component heights.
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.
last.str, stem strings used for str() specifying how the last branch (at each level) should start and the stem to use for each dendrogram branch.

Details

This documentation is somewhat 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]], or shorter z[[c(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(), and since R 2.13.0, there is also a as.hclust() method as an inverse.

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

The merge(x,y, ...) method allows to join two (or more!) dendrograms into a new one which has x and y (and optional further arguments) as branches.

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

plot():
When using type = "triangle", center = TRUE often looks better.
str(d):
If you really want to see the internal structure, use str(unclass(d)) instead.

See Also

dendrapply for applying a function to each node. order.dendrogram and reorder.dendrogram; further, the labels method.

Examples

require(graphics); require(utils)

hc <- hclust(dist(USArrests), "ave")
(dend1 <- as.dendrogram(hc)) # "print()" method
str(dend1)          # "str()" method
str(dend1, max = 2, last.str= "'") # 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)

## simple test for as.hclust() as the inverse of as.dendrogram():
stopifnot(identical(as.hclust(dend1)[1:4], hc[1:4]))

dend2 <- cut(dend1, h=70)
plot(dend2$upper)
## leaves are wrong horizontally:
plot(dend2$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$lower[[2]], nodePar=list(col=1),# non empty list
     edgePar = list(lty=1:2, col=2:1), edge.root=TRUE)
par(op)
d3 <- dend2$lower[[2]][[2]][[1]]
stopifnot(identical(d3, dend2$lower[[2]][[c(2,1)]]))
str(d3, last.str="'")

## merge() to join dendrograms:
(d13 <- merge(dend2$lower[[1]], dend2$lower[[3]]))
## merge() all parts back (using default 'height' instead of original one):
den.1 <- Reduce(merge, dend2$lower)
## or merge() all four parts at same height --> 4 branches (!)
d. <- merge(dend2$lower[[1]], dend2$lower[[2]], dend2$lower[[3]],
            dend2$lower[[4]])
## (with a warning) or the same using  do.call :
stopifnot(identical(d., do.call(merge, dend2$lower)))
plot(d., main="merge(d1, d2, d3, d4)  |->  dendrogram with a 4-split")

## "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")




[Package stats version 2.13.1 Index]