ape: def – R documentation

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def

Definition of Vectors for Plotting or Annotating

Description

This function can be used to define vectors to annotate a set of taxon names, labels, etc. It should facilitate the (re)definition of colours or similar attributes for plotting trees or other graphics.

Usage

def(x, ..., default = NULL, regexp = FALSE)

Arguments

`x`	a vector of mode character.
`...`	a series of statements defining the attributes.
`default`	the default to be used (see details).
`regexp`	a logical value specifying whether the statements defined in `...` should be taken as regular expressions.

Details

The idea of this function is to make the definition of colours, etc., simpler than what is done usually. A typical use is:

def(tr$tip.label, Homo_sapiens = "blue")

which will return a vector of character strings all "black" except one matching the tip label "Homo_sapiens" which will be "blue". Another use could be:

def(tr$tip.label, Homo_sapiens = 2)

which will return a vector a numerical values all 1 except for "Homo_sapiens" which will be 2. Several definitions can be done, e.g.:

def(tr$tip.label, Homo_sapiens = "blue", Pan_paniscus = "red")

The default value is determined with respect to the mode of the values given with the ... (either "black" or 1).

If regexp = TRUE is used, then the names of the statements must be quoted, e.g.:

def(tr$tip.label, "^Pan_" = "red", regexp = TRUE)

will return "red" for all labels starting with "Pan_".

Value

a vector of the same length than x.

Author(s)

Emmanuel Paradis

Examples

data(bird.orders)
a <- def(bird.orders$tip.label, Galliformes = 2)
str(a) # numeric
plot(bird.orders, font = a)
co <- def(bird.orders$tip.label, Passeriformes = "red", Trogoniformes = "blue")
str(co) # character
plot(bird.orders, tip.color = co)
### use of a regexp (so we need to quote it) to colour all orders
### with names starting with "C" (and change the default):
co2 <- def(bird.orders$tip.label, "^C" = "gold", default = "grey", regexp = TRUE)
plot(bird.orders, tip.color = co2)

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

def