dendextend (version 1.13.4)

shuffle: 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, ...)
# S3 method for default
shuffle(dend, ...)
# S3 method for dendrogram
shuffle(dend, ...)
# S3 method for dendlist
shuffle(dend, which, ...)
# S3 method for hclust
shuffle(dend, ...)
# S3 method for 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

Value

A randomlly rotated tree object

Details

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

See Also

tanglegram, entanglement, rotate

Examples

# NOT RUN {
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)
# }