% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/untangle.R
\name{untangle_step_rotate_2side}
\alias{untangle_step_rotate_2side}
\title{Stepwise untangle two trees one at a time}
\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{
\item{dend1}{a dendrogram object. The one we will rotate to best fit
dend2.}

\item{dend2}{a dendrogram object. The one we will rotate to best fit
dend1.}

\item{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 \link{entanglement}).}

\item{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".}

\item{max_n_iterations}{integer. The maximal number of times to switch between optimizing one tree with another.}

\item{print_times}{logical (TRUE), should we print how many times we switched between rotating the two trees?}

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

\item{...}{not used}
}
\value{
A list with two dendrograms (dend1/dend2), 
after they are rotated to best fit one another.
}
\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 \link{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.
}
\examples{

\dontrun{
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.

}                              
}
\seealso{
\link{tanglegram}, \link{match_order_by_labels},
\link{entanglement}, \link{flip_leaves}, \link{all_couple_rotations_at_k}.
\link{untangle_step_rotate_1side}.
}
