phylogram (version 1.0.0)

prune: Remove tree nodes by regular expression pattern matching.

Description

"prune" takes an object of class "dendrogram" and removes all branches whose branch labels match a given regular expression.

Usage

prune(tree, pattern, invert = FALSE, untag = FALSE, ...)

Arguments

tree

an object of class "dendrogram".

pattern

a regular expression.

invert

logical indicating whether the branches whose labels match the regular expression provided in "pattern" should be discarded and the others kept (FALSE; default) or vice versa. Nodes without "label" attributes are ignored.

untag

logical (used only when invert = TRUE). Indicates whether the specified pattern should be removed from the branch labels in the returned object.

...

further arguments to be passed to grepl and gsub.

Value

Returns an object of class "dendrogram".

Details

This function recursively tests the "label" attribute of each dendrogram node (including non-leaf inner nodes if applicable) for the specified pattern, removing those that register a positive hit. Note that positive matching inner nodes are removed along with all of their sub-nodes, regardless of whether the "label" attributes of the sub-nodes match the pattern.

See Also

The drop.tip function in the ape package performs a similar operation for objects of class "phylo". See regex for help with compiling regular expressions.

Examples

  x <- read.dendrogram(text = "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);")
  plot(x, horiz = TRUE)
  x <- prune(x, pattern = "^A$")
  plot(x, horiz = TRUE)