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dendextend (version 1.18.1)

seriate_dendrogram: Rotates a dendrogram based on a seriation of a distance matrix

Description

Rotates a dendrogram so it confirms to an order of a provided distance object. The seriation algorithm is based on seriate, which tries to find a linear order for objects using data in form of a dissimilarity matrix (one mode data).

This is useful for heatmap visualization.

Usage

seriate_dendrogram(dend, x, method = c("OLO", "GW"), ...)

Value

A dendrogram that is rotated based on the optimal ordering of the distance matrix

Arguments

dend

An object of class dendrogram or hclust

x

a dist object.

method

a character vector of either "OLO" or "GW": "OLO" - Optimal leaf ordering, optimzes the Hamiltonian path length that is restricted by the dendrogram structure - works in O(n^4) "GW" - Gruvaeus and Wainer heuristic to optimze the Hamiltonian path length that is restricted by the dendrogram structure

...

parameters passed to seriate

See Also

rotate, seriate

Examples

Run this code
if (FALSE) {
# library(dendextend)
d <- dist(USArrests)
hc <- hclust(d, "ave")
dend <- as.dendrogram(hc)

heatmap(as.matrix(USArrests))

dend2 <- seriate_dendrogram(dend, d)
heatmap(as.matrix(USArrests), Rowv = dend)
}

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