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.

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

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

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

# S3 method for 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.

See also

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

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

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

Author

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

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)