DECIPHER (version 2.0.2)

ReadDendrogram: 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.

Value

An object of class dendrogram.

Details

ReadDendrogram will create a dendrogram object from a Newick formatted tree. Note that all edge lengths must be specified, but labels are optional.

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", asDendrogram=TRUE)
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)