dendrogram {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.

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

Usage

as.dendrogram(object, ...)
## S3 method for class 'dendrogram'
plot(x, type=c("rectangle", "triangle"),
         center=FALSE, edge.root= !is.null(attr(x,"edgetext")),
         nodePar = NULL, edgePar = list(), xlab="", ylab="",
         horiz = FALSE, ...)
## S3 method for class 'dendrogram'
cut(x, h, ...)
## S3 method for class 'dendrogram'
print(x, digits, ...)
## S3 method for class 'dendrogram'
str(x, ...)

Arguments

object	any R object that can be made into one of class "dendrogram".
x	object of class "dendrogram".
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 (see lines). The list may contain components named col, lty and/or lwd.
horiz	logical indicating if the dendrogram should be draw horizontally or not.
h	height at which the tree is cut.
..., xlab, ylab	graphical parameters, or arguments for other methods.
digits	integer specifiying the precision for printing, see print.default.

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:

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 of the branch. This is needed at least for plot(*, center=FALSE).

text

character; the label of the node

edgetext

character; the label for the edge leading to the node

nodePar

a named list of length one vectors specifying node-specific attributes for points plotting, see the nodePar argument above.

edgePar

a named list of length one vectors specifying attributes for segments plotting of the edge leading to the node, see the edgePar argument above.

leaf

logical, if TRUE, the node is a leaf of the tree. This will often be a character which can be used for plotting instead of the text attribute.

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.

isLeaf(), plotNode() and plotNodeLimit() are helper functions.

Note

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

Examples

library(mva)
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)