R: Rotates a dendrogram based on a seriation of a distance...

seriate_dendrogram {dendextend} | R Documentation

## 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"), ...)

### 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

### Value

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

### See Also

`rotate`, seriate

### Examples

    ## Not run:
    # 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)

    ## End(Not run)

[Package dendextend version 1.8.0 Index]