order.optimal: Optimal Leaf Ordering of Binary Trees.

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/order.r

Description

Find an optimal linear leaf ordering of a binary merge tree as produced by a hierarchical cluster algorithm.

Usage

1

Arguments

dist

an object of class dist.

merge

a binary merge tree (see hclust).

Details

A binary tree has 2^(n-1) internal nodes (subtrees) and the same number of leaf orderings. That is, at each internal node the left and right subtree (or leaves) can be swapped, or, in terms of a dendrogram, be flipped.

An objective measure of a leaf ordering is the sum of the distances along the path connecting the leaves in the given order. An ordering with a minimal path length is defined to be an optimal ordering.

This function provides an interface to the optimal leaf ordering algorithm (see references) for tree representations that are used by hierarchical cluster algorithms such as hclust.

Note that non-finite distance values are not allowed.

Value

A list with the following components:

merge

a matrix containing the merge tree corresponding with the optimal leaf order.

order

a vector containing the optimal leaf order.

length

the length of the ordering.

Note

The time complexity of the algorithm is O(n^3).

Author(s)

Christian Buchta

References

Z. Bar-Joseph, E. D. Demaine, D. K. Gifford, and T. Jaakkola. (2001). Fast Optimal Leaf Ordering for Hierarchical Clustering. Bioinformatics, Vol. 17 Suppl. 1, pp. 22-29.

See Also

hclust for hierarchical clustering and order.length for computing the objective value of a leaf ordering.

Examples

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d <- dist(matrix(runif(30), ncol=2))
hc <- hclust(d)
co <- order.optimal(d, hc$merge)
### compare dendrograms
ho <- hc
ho$merge <- co$merge
ho$order <- co$order
op <- par(mfrow=c(2,2), pty="s")
plot(hc, main="hclust")
plot(ho, main="optimal")
# compare images
implot(d[[hc$order]])
implot(d[[co$order]])
par(op)
### compare lengths
order.length(d, hc$order)
order.length(d, co$order)
cat("compare: ",co$length,"\n")

cba documentation built on May 29, 2017, 10:32 p.m.

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