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Reorder Dendrograms using Optimal Leaf Ordering

Source: R/reorder.hclust.R
reorder.hclust.Rd

Reorder method for dendrograms for optimal leaf ordering.

Usage

# S3 method for class 'hclust'
reorder(x, dist, method = "OLO", ...)

Arguments

x

an object of class hclust.

dist

an object of class dist with dissimilarities between the objects in x.

method

a character string with the name of the used measure. Available are:

  • "OLO" (optimal leaf ordering; Bar-Joseph et al., 2001) implemented in this package and

  • "GW" (Gruvaeus and Wainer, 1972) from package gclus.

...

further arguments are currently ignored.

Value

A reordered hclust object.

Details

Minimizes the distance between neighboring objects (leaf nodes) in the dendrogram by flipping the order of subtrees. The algorithm by Gruvaeus and Wainer is implemented in package gclus (Hurley 2004).

References

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

Gruvaeus, G. and Wainer, H. (1972): Two Additions to Hierarchical Cluster Analysis, British Journal of Mathematical and Statistical Psychology, 25, 200–206.

Hurley, Catherine B. (2004): Clustering Visualizations of Multidimensional Data. Journal of Computational and Graphical Statistics, 13(4), 788–806.

See also

gclus::reorder.hclust()

Other permutation: get_order(), permutation_vector2matrix(), permute(), ser_dist(), ser_permutation(), ser_permutation_vector()

Author

Michael Hahsler

Examples

## cluster European cities by distance
data("eurodist")
d <- as.dist(eurodist)
hc <- hclust(eurodist)

## plot original dendrogram and the reordered dendrograms
plot(hc)

plot(reorder(hc, d, method = "GW"))

plot(reorder(hc, d, method = "OLO"))