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

Description Usage Arguments Value See Also Examples

View source: R/seriate_dendrogram.R

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

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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

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## 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)

Example output

---------------------
Welcome to dendextend version 1.5.2
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
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Attaching package: 'dendextend'

The following object is masked from 'package:stats':

    cutree

Loading required namespace: seriation

dendextend documentation built on Oct. 19, 2018, 9:03 a.m.