ReadDendrogram: Read a Dendrogram from a Newick Formatted File

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

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 [e-mail]

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)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: RSQLite

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DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.