shuffle: Random rotation of trees

In dendextend: Extending 'dendrogram' Functionality in R

Random rotation of trees

Description

'shuffle' randomilly rotates ("shuffles") a tree, changing its presentation while preserving its topolgoy. 'shuffle' is based on rotate and through its methods can work for any of the major tree objects in R (dendrogram/hclust/phylo).

This function is useful in combination with tanglegram and entanglement.

Usage

shuffle(dend, ...)

## Default S3 method:
shuffle(dend, ...)

## S3 method for class 'dendrogram'
shuffle(dend, ...)

## S3 method for class 'dendlist'
shuffle(dend, which, ...)

## S3 method for class 'hclust'
shuffle(dend, ...)

## S3 method for class 'phylo'
shuffle(dend, ...)

Arguments

dend	a tree object (dendrogram/hclust/phylo)
...	Ignored.
which	an integer vector for indicating which of the trees in the dendlist object should be plotted default is missing, in which case all the dends in dendlist will be shuffled

Details

'shuffle' is a function that randomilly rotates ("shuffles") a tree. a dendrogram leaves order (by means of rotation)

Value

A randomlly rotated tree object

See Also

tanglegram, entanglement, rotate

Examples

dend <- USArrests %>%
  dist() %>%
  hclust() %>%
  as.dendrogram()
set.seed(234238)
dend2 <- shuffle(dend)

tanglegram(dend, dend2, margin_inner = 7)
entanglement(dend, dend2) # 0.3983

# although these ARE the SAME tree:
tanglegram(sort(dend), sort(dend2), margin_inner = 7)

dendextend documentation built on March 31, 2023, 10:17 p.m.