Consensus without taxa
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 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", ...)
trees |
A list of phylogenetic trees, of class |
tip |
A character vector specifying the names (or numbers) of tips to
drop (using |
... |
Additional parameters to pass on to |
position |
Where to plot the missing taxa.
See |
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.
Martin R. Smith (martin.smith@durham.ac.uk)
Other tree manipulation:
AddTip(),
CollapseNode(),
DropTip(),
EnforceOutgroup(),
LeafLabelInterchange(),
MakeTreeBinary(),
RenumberTips(),
RenumberTree(),
Renumber(),
RootTree(),
SingleTaxonTree(),
SortTree(),
Subtree()
Other tree properties:
NSplits(),
NTip(),
SplitsInBinaryTree(),
TipLabels(),
TreeIsRooted()
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.