ReadDendrogram {DECIPHER}

R Documentation

Read a Dendrogram from a Newick Formatted File

Description

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

Usage

ReadDendrogram(file,
               convertBlanks = TRUE,
               internalLabels = TRUE,
               keepRoot = TRUE)

Arguments

file	a connection object or a character string.
convertBlanks	Logical specifying whether to convert underscores in unquoted leaf labels to spaces.
internalLabels	Logical indicating whether to keep internal node labels as “edgetext” preceding the node in the dendrogram.
keepRoot	Logical specifying whether to keep the root node (if one is present) as a dendrogram leaf.

Details

ReadDendrogram will create a dendrogram object from a Newick formatted tree. Note that all edge lengths must be specified, but labels are optional. Leaves will be numbered by their labels in alphabetical order.

Value

An object of class dendrogram.

Author(s)

Erik Wright eswright@pitt.edu

See Also

IdClusters, WriteDendrogram

Examples

tf <- tempfile()
dists <- matrix(c(0, 10, 20, 10, 0, 5, 20, 5, 0),
    nrow=3,
    dimnames=list(c("dog", "elephant", "horse")))
dend1 <- IdClusters(dists, method="NJ", type="dendrogram")
WriteDendrogram(dend1, file=tf)

dend2 <- ReadDendrogram(tf)
layout(matrix(1:2))
plot(dend1, main="Dendrogram Written")
plot(dend2, main="Dendrogram Read")

unlink(tf)

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