ape (version 5.1)

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.

Value

a vector of the same length than x.

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_".

Examples

# NOT RUN {
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)
# }