dendextend: all_couple_rotations_at_k – R documentation

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all_couple_rotations_at_k

Rotate tree branches for k

Description

Given a tree and a k number of clusters, the tree is rotated so that the extra clusters added from k-1 to k clusters are flipped.

This is useful for finding good trees for a tanglegram.

Usage

all_couple_rotations_at_k(dend, k, dend_heights_per_k, ...)

Arguments

`dend`	a dendrogram object
`k`	integer scalar with the number of clusters the tree should be cut into.
`dend_heights_per_k`	a named vector that resulted from running heights_per_k.dendrogram. When running the function many times, supplying this object will help improve the running time if using the cutree.dendrogram method..
`...`	not used

Value

A list with dendrogram objects with all the possible rotations for k clusters (beyond the k-1 clusters!).

Examples

## Not run: 
dend1 <- USArrests[1:5, ] %>%
  dist() %>%
  hclust() %>%
  as.dendrogram()
dend2 <- all_couple_rotations_at_k(dend1, k = 2)[[2]]
tanglegram(dend1, dend2)
entanglement(dend1, dend2, L = 2) # 0.5

dend2 <- all_couple_rotations_at_k(dend1, k = 3)[[2]]
tanglegram(dend1, dend2)
entanglement(dend1, dend2, L = 2) # 0.4

dend2 <- all_couple_rotations_at_k(dend1, k = 4)[[2]]
tanglegram(dend1, dend2)
entanglement(dend1, dend2, L = 2) # 0.05

## End(Not run)

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