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.

### 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")

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

    unlink(tf)

[Package DECIPHER version 2.12.0 Index]