R: Stepwise untangle two trees one at a time

untangle_step_rotate_2side {dendextend} | R Documentation

## Stepwise untangle two trees one at a time

### Description

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.

It goes through rotating dend1, then dend2, and so on - until a locally optimal solution is found.

Similar to "step1side", one tree is held fixed and the other tree is rotated. 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 iterations. Once finished the rotated tree is held fixed, and the fixed tree is now rotated. This continues until a local optimal solution is reached.

### Usage

    untangle_step_rotate_2side(dend1, dend2, L = 1.5, direction = c("forward",
      "backward"), max_n_iterations = 10L,
      print_times = dendextend_options("warn"), k_seq = NULL, ...)

### Arguments

`dend1` | a dendrogram object. The one we will rotate to best fit dend2.
`dend2` | a dendrogram object. The one we will rotate to best fit dend1.
`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 overrides "direction".
`max_n_iterations` | integer. The maximal number of times to switch between optimizing one tree with another.
`print_times` | logical (TRUE), should we print how many times we switched between rotating the two trees?
`k_seq` | a sequence of k clusters to go through for improving dend1. If NULL (default), then we use the "direction" parameter.
`...` | not used

### Value

A list with two dendrograms (dend1/dend2), after they are rotated to best fit one another.

### See Also

tanglegram, match_order_by_labels, entanglement, flip_leaves, all_couple_rotations_at_k. untangle_step_rotate_1side.

### Examples

    ## Not run:
    dend1 <- USArrests[1:20,] %>% dist %>% hclust %>% as.dendrogram
    dend2 <- USArrests[1:20,] %>% dist %>% hclust(method = "single") %>% as.dendrogram
    set.seed(3525)
    dend2 <- shuffle(dend2)
    tanglegram(dend1,dend2, margin_inner=6.5)
    entanglement(dend1,dend2, L = 2) # 0.79

    dend2_corrected <- untangle_step_rotate_1side(dend2, dend1)
    tanglegram(dend1,dend2_corrected, margin_inner=6.5) # Good.
    entanglement(dend1,dend2_corrected, L = 2) # 0.0067
    # it is better, but not perfect. Can we improve it?

    dend12_corrected <- untangle_step_rotate_2side(dend1, dend2)
    tanglegram(dend12_corrected[[1]],dend12_corrected[[2]], margin_inner=6.5) # Better...
    entanglement(dend12_corrected[[1]],dend12_corrected[[2]], L=2) # 0.0045

    # best combination:
    dend12_corrected_1 <- untangle_random_search(dend1, dend2)
    dend12_corrected_2 <- untangle_step_rotate_2side(dend12_corrected_1[[1]],dend12_corrected_1[[2]])
    tanglegram(dend12_corrected_2[[1]],dend12_corrected_2[[2]], margin_inner=6.5) # Better...
    entanglement(dend12_corrected_2[[1]],dend12_corrected_2[[2]], L=2) # 0 - PERFECT.

    ## End(Not run)

[Package dendextend version 1.8.0 Index]