DECIPHER (version 2.0.2)

WriteDendrogram: Write a Dendrogram to Newick Format

Description

Writes a dendrogram object to a file in Newick (also known as New Hampshire) parenthetic format.

Usage

WriteDendrogram(x, file = "", quoteLabels = TRUE, convertBlanks = !quoteLabels, internalLabels = TRUE, digits = 10, append = FALSE)

Arguments

x

An object of class dendrogram.

file

A connection or a character string naming the file path where the tree should be exported. If "" (the default), the tree is printed to the standard output connection, the console unless redirected by sink.

quoteLabels

Logical specifying whether to place leaf labels in double quotes.

convertBlanks

Logical specifying whether to convert spaces in leaf labels to underscores.

internalLabels

Logical indicating whether to write any ``edgetext'' preceding a node as an internal node label.

digits

The maximum number of digits to print for edge lengths.

append

Logical indicating whether to append to an existing file. Only applicable if file is a character string. If FALSE (the default), then the file is overwritten.

Value

NULL.

Details

WriteDendrogram will write a dendrogram object to a file in standard Newick format. Note that special characters (commas, square brackets, colons, semi-colons, and parentheses) present in leaf labels will likely cause a broken Newick file unless quoteLabels is TRUE (the default).

See Also

IdClusters, ReadDendrogram

Examples

dists <- matrix(c(0, 10, 20, 10, 0, 5, 20, 5, 0),
    nrow=3,
    dimnames=list(c("dog", "elephant", "horse")))
dend <- IdClusters(dists, method="NJ", asDendrogram=TRUE)
WriteDendrogram(dend)