dendextend: find_dend – R documentation

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find_dend

Finds a "good" dendrogram for a dist

Description

There are many options for choosing distance and linkage functions for hclust. This function goes through various combinations of the two and helps find the one that is most "similar" to the original distance matrix.

Usage

dend_expend(
  x,
  dist_methods = c("euclidean", "maximum", "manhattan", "canberra", "binary",
    "minkowski"),
  hclust_methods = c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty",
    "median", "centroid"),
  hclust_fun = hclust,
  optim_fun = cor_cophenetic,
  ...
)

find_dend(x, ...)

Arguments

`x`	A matrix or a data.frame. Can also be a dist object.
`dist_methods`	A vector of possible dist methods.
`hclust_methods`	A vector of possible hclust methods.
`hclust_fun`	By default hclust.
`optim_fun`	A function that accepts a dend and a dist and returns how the two are in agreement. Default is cor_cophenetic.
`...`	options passed from find_dend to dend_expend.

Value

dend_expend: A list with three items. The first item is called "dends" and includes a dendlist with all the possible dendrogram combinations. The second is "dists" and includes a list with all the possible distance matrix combination. The third. "performance", is data.frame with three columns: dist_methods, hclust_methods, and optim. optim is calculated (by default) as the cophenetic correlation (see: cor_cophenetic) between the distance matrix and the cophenetic distance of the hclust object.

find_dend: A dendrogram which is "optimal" based on the output from dend_expend.

Examples

x <- datasets::mtcars
out <- dend_expend(x, dist_methods = c("euclidean", "manhattan"))
out$performance

dend_expend(dist(x))$performance

best_dend <- find_dend(x, dist_methods = c("euclidean", "manhattan"))
plot(best_dend)

dendextend

Extending 'dendrogram' Functionality in R

v1.15.1

GPL-2 | GPL-3

Authors

Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Yoav Benjamini [ths], Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Ben Ho [ctb] (https://github.com/SplitInf), Samuel Perreault [ctb] (https://github.com/samperochkin), Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/), David Bradley [ctb] (https://github.com/DBradley27), Houyun Huang [ctb] (https://github.com/houyunhuang)

Initial release

2021-05-08