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'
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 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.
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")

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