Sort tree
SortTree() sorts each node into a consistent order, so that node rotation
does not obscure similarities between similar trees.
SortTree(tree) ## S3 method for class 'phylo' SortTree(tree) ## S3 method for class 'list' SortTree(tree) ## S3 method for class 'multiPhylo' SortTree(tree)
tree |
One or more trees of class |
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).
SortTree() returns tree in the format of tree, with each node
in each tree sorted such that the larger clade is first.
Martin R. Smith (martin.smith@durham.ac.uk)
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()
messyTree <- as.phylo(10, 6) plot(messyTree) sorted <- SortTree(messyTree) plot(sorted) ape::nodelabels() ape::edgelabels()
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