TreeTools (version 1.4.4)

SortTree: Sort tree

Description

SortTree() sorts each node into a consistent order, so that node rotation does not obscure similarities between similar trees.

Usage

SortTree(tree)
# S3 method for phylo
SortTree(tree)
# S3 method for list
SortTree(tree)
# S3 method for multiPhylo
SortTree(tree)

Arguments

tree

One or more trees of class phylo, optionally as a list or a multiPhylo object.

Value

SortTree() returns tree in the format of tree, with each node in each tree sorted such that the larger clade is first.

Details

At each node, clades will be listed in tree$edge in decreasing size order.

Clades that contain the same number of leaves are sorted in decreasing order of minimum leaf number, so (2, 3) will occur before (1, 4).

As trees are plotted from 'bottom up', the largest clades will 'sink' to the bottom of a plotted tree.

tree must (presently) be binary (#25).

See Also

Preorder() also rearranges trees into a consistent shape, but based on the index of leaves rather than the size of subtrees.

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), EnforceOutgroup(), LeafLabelInterchange(), MakeTreeBinary(), RenumberTips(), RenumberTree(), Renumber(), RootTree(), SingleTaxonTree(), Subtree()

Examples

# NOT RUN {
messyTree <- as.phylo(10, 6)
plot(messyTree)

sorted <- SortTree(messyTree)
plot(sorted)
ape::nodelabels()
ape::edgelabels()

# }