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.
a vector of mode character.
a series of statements defining the attributes.
the default to be used (see details).
a logical value specifying whether the statements
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$tip.label, Homo_sapiens = "blue", Pan_paniscus = "red")
The default value is determined with respect to the mode of the values
given with the
... (either "black" or 1).
regexp = TRUE is used, then the names of the statements must be
def(tr$tip.label, "^Pan_" = "red", regexp = TRUE)
will return "red" for all labels starting with "Pan_".
a vector of the same length than
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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)
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