Random rotation of trees
'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.
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, ...)
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 |
'shuffle' is a function that randomilly rotates ("shuffles") a tree. a dendrogram leaves order (by means of rotation)
A randomlly rotated tree object
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)
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