# def

From ape v3.2
0th

Percentile

##### Definition of Vectors for Plotting or Annotating

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.

Keywords
manip
##### 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 will:

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")

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

##### Value

• a vector of the same length than x.

• def
##### 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)
Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)

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