R: Sort tree

SortTree {TreeTools} | R Documentation

## 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 class 'phylo'
    SortTree(tree)

    ## S3 method for class 'list'
    SortTree(tree)

    ## S3 method for class 'multiPhylo'
    SortTree(tree)

### Arguments

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

### 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).

### Value

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

### Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

### 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

    messyTree <- as.phylo(10, 6)
    plot(messyTree)

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

[Package TreeTools version 1.4.4 Index]