makeLabel

0th

Percentile

Label Management

This is a generic function with methods for character vectors, trees of class "phylo", lists of trees of class "multiPhylo", and DNA sequences of class "DNAbin". All options for the class character may be used in the other methods.

Keywords
manip
Usage
makeLabel(x, ...)
## S3 method for class 'character':
makeLabel(x, len = 99, space = "_", make.unique = TRUE,
          illegal = "():;,[]", quote = FALSE, ...)
## S3 method for class 'phylo':
makeLabel(x, tips = TRUE, nodes = TRUE, ...)
## S3 method for class 'multiPhylo':
makeLabel(x, tips = TRUE, nodes = TRUE, ...)
## S3 method for class 'DNAbin':
makeLabel(x, ...)
Details

The option make.unique does not work exactly in the same way then the function of the same name: numbers are suffixed to all labels that are identical (without separator). See the examples.

If there are 10--99 identical labels, the labels returned are "xxx01", "xxx02", etc, or "xxx001", "xxx002", etc, if they are 100--999, and so on. The number of digits added preserves the option `len'.

The default for `len' makes labels short enough to be read by PhyML. Clustal accepts labels up to 30 character long.

Value

An object of the appropriate class.

Note

The current version does not perform well when trying to make very short unique labels (e.g., less than 5 character long).

See Also

makeNodeLabel, make.unique, make.names, abbreviate, mixedFontLabel

Aliases
Examples
x <- rep("a", 3)
makeLabel(x)
make.unique(x) # <- from R's base
x <- rep("aaaaa", 2)
makeLabel(x, len = 3) # made unique and of length 3
makeLabel(x, len = 3, make.unique = FALSE)
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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