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

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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.

Value

An object of class dendrogram.

Author(s)

Erik Wright DECIPHER@cae.wisc.edu

See Also

IdClusters, WriteDendrogram

Examples

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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")

# Note that the ordering information is lost
any(unlist(dend1) != unlist(dend2)) # TRUE

unlink(tf)

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