ape: makeNodeLabel – R documentation

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ape

makeNodeLabel

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:

“number”The labels are created with 1, 2, ... prefixed with the argument prefix; thus the default is to have Node1, Node2, ... Set prefix = "" to have only numbers.
“md5sum”For each node, the labels of the tips descendant from this node are extracted, sorted alphabetically, and written into a temporary file, then the md5sum of this file is extracted and used as label. This results in a 32-character string which is unique (even accross trees) for a given set of tip labels.
“user”the argument nodeList must be a list with names, the latter will be used as node labels. For each element of nodeList, the tip labels of the tree are searched for patterns present in this element: this is done using grep. Then the most recent common ancestor of the matching tips is given the corresponding names as labels. This is repeated for each element of nodeList.

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

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)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24