reorder.hclust

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Reorder Dendrograms using Optimal Leaf Ordering

Reorder method for dendrograms for optimal leaf ordering.

Keywords
cluster, optimize
Usage
# S3 method for 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) and "GW" (Gruvaeus and Wainer, 1972).
...
further arguments are currently ignored.
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).

Value

A reordered hclust object.

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

reorder.hclust

Aliases
  • reorder
  • reorder.hclust
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"))  
Documentation reproduced from package seriation, version 1.2-2, License: GPL-3

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