ConsensusWithout: Reduced consensus, omitting specified taxa

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Reduced consensus, omitting specified taxa

Description

ConsensusWithout() displays a consensus plot with specified taxa excluded, which can be a useful way to increase the resolution of a consensus tree when a few wildcard taxa obscure a consistent set of relationships. MarkMissing() adds missing taxa as loose leaves on the plot.

Usage

ConsensusWithout(trees, tip = character(0), ...)

## S3 method for class 'phylo'
ConsensusWithout(trees, tip = character(0), ...)

## S3 method for class 'multiPhylo'
ConsensusWithout(trees, tip = character(0), ...)

## S3 method for class 'list'
ConsensusWithout(trees, tip = character(0), ...)

MarkMissing(tip, position = "bottomleft", ...)

Arguments

trees	A list of phylogenetic trees, of class multiPhylo or list.
tip	A character vector specifying the names (or numbers) of tips to drop (using ape::drop.tip()).
...	Additional parameters to pass on to ape::consensus() or legend().
position	Where to plot the missing taxa. See legend() for options.

Value

ConsensusWithout() returns a consensus tree (of class phylo) without the excluded taxa.

MarkMissing() provides a null return, after plotting the specified tips as a legend.

Author(s)

Martin R. Smith ([e-mail])

See Also

Other tree manipulation: AddTip(), CollapseNode(), DropTip(), EnforceOutgroup(), ImposeConstraint(), KeptPaths(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), Renumber(), RenumberTips(), RenumberTree(), RootTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Other tree properties: MatchEdges(), NSplits(), NTip(), NodeNumbers(), PathLengths(), SplitsInBinaryTree(), TipLabels(), TreeIsRooted()

Other consensus tree functions: Consensus(), RoguePlot()

Examples

oldPar <- par(mfrow = c(1, 2), mar = rep(0.5, 4))

# Two trees differing only in placement of tip 2:
trees <- as.phylo(c(0, 53), 6)
plot(trees[[1]])
plot(trees[[2]])

# Strict consensus (left panel) lacks resolution:
plot(ape::consensus(trees))

# But omitting tip two (right panel) reveals shared structure in common:
plot(ConsensusWithout(trees, "t2"))
MarkMissing("t2")

par(oldPar)

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.