makeNodeLabel {ape}R Documentation

Makes Node Labels

Description

This function makes node labels in a tree in a flexible way.

Usage

makeNodeLabel(phy, method = "number", prefix = "Node", nodeList = list(), ...)

Arguments

phy

an object of class "phylo".

method

a character string giving the method used to create the labels. Three choices are possible: "number" (the default), "md5sum", and "user", or any unambiguous abbreviation of these.

prefix

the prefix used if method = "number".

nodeList

a named list specifying how nodes are names if method = "user" (see details and examples).

...

further arguments passed to grep.

Details

The three methods are described below:

The method "user" can be used in combination with either of the two others (see examples). Note that this method only modifies the specified node labels (so that if the other nodes have already labels they are not modified) while the two others change all labels.

Value

an object of class "phylo".

Author(s)

Emmanuel Paradis

See Also

makeLabel, grep, mixedFontLabel, label2table, checkLabel

Examples

tr <-
"((Pan_paniscus,Pan_troglodytes),((Homo_sapiens,Homo_erectus),Homo_abilis));"
tr <- read.tree(text = tr)
tr <- makeNodeLabel(tr, "u", nodeList = list(Pan = "Pan", Homo = "Homo"))
plot(tr, show.node.label = TRUE)
### does not erase the previous node labels:
tr <- makeNodeLabel(tr, "u", nodeList = list(Hominid = c("Pan","Homo")))
plot(tr, show.node.label = TRUE)
### the two previous commands could be combined:
L <- list(Pan = "Pan", Homo = "Homo", Hominid = c("Pan","Homo"))
tr <- makeNodeLabel(tr, "u", nodeList = L)
### combining different methods:
tr <- makeNodeLabel(tr, c("n", "u"), prefix = "#", nodeList = list(Hominid = c("Pan","Homo")))
plot(tr, show.node.label = TRUE)

[Package ape version 5.5 Index]