dendextend (version 0.14.2)

untangle_step_rotate_1side: Stepwise untangle one tree compared to another

Description

Given a fixed tree and a tree we wish to rotate, this function goes through all of the k number of clusters (from 2 onward), and each time rotates the branch which was introduced in the new k'th cluster. This rotated tree is compared with the fixed tree, and if it has a better entanglement, it will be used for the following interations. This is a greedy forward selection algorithm for rotating the tree and looking for a better match. This is useful for finding good trees for a tanglegram.

Usage

untangle_step_rotate_1side(dend1, dend2_fixed, L = 1.5,
  direction = c("forward", "backward"), k_seq = NULL, dend_heights_per_k,
  ...)

Arguments

dend1

a dendrogram object. The one we will rotate to best fit dend2_fixed.

dend2_fixed

a dendrogram object. This one is kept fixed.

L

the distance norm to use for measuring the distance between the two trees. It can be any positive number, often one will want to use 0, 1, 1.5, 2 (see 'details' in entanglement).

direction

a character scalar, either "forward" (default) or "backward". Impacts the direction of clustering that are tried. Either from 2 and up (in case of "forward"), or from nleaves to down (in case of "backward") If k_seq is not NULL, then it o

k_seq

a sequence of k clusters to go through for improving dend1. If NULL (default), then we use the "direction" parameter.

dend_heights_per_k

a numeric vector of values which indicate which height will produce which number of clusters (k)

...

not used

Value

• dend1 after it was rotated to best fit dend2_fixed.

See Also

tanglegram, match_order_by_labels, entanglement, flip_leaves, all_couple_rotations_at_k, untangle_step_rotate_2side.

Examples

dend1 <- as.dendrogram(hclust(dist(USArrests[1:10,])))
set.seed(3525)
dend2 <- shuffle(dend1)
tanglegram(dend1,dend2)
entanglement(dend1,dend2, L = 2) # 0.4727

dend2_corrected <- untangle_step_rotate_1side(dend2, dend1)
tanglegram(dend1,dend2_corrected) # FIXED.
entanglement(dend1,dend2_corrected, L = 2) # 0