ReadDendrogram: Read a Dendrogram from a Newick Formatted File

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/ReadDendrogram.R

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 [email protected]

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)

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, cbind, colMeans, colSums, colnames, 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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Time difference of 0.15 secs

[1] TRUE

DECIPHER documentation built on May 10, 2018, 6 p.m.