TreeTools (version 0.1.3)

ConsensusWithout: Consensus without taxa

Description

Displays a consensus plot with selected taxa excluded.

Usage

ConsensusWithout(trees, tip, ...)

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.

Functions

  • MarkMissing: Adds labels for taxa omitted from a plotted consensus tree.

Details

A useful way to gain resolution if a few wildcard taxa obscure a consistent set of relationship.

Examples

Run this code
# NOT RUN {
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 lacks resolution:
plot(ape::consensus(trees))

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

par(oldPar)

# }

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