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

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(DECIPHER)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: RSQLite
Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DECIPHER/ReadDendrogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ReadDendrogram
> ### Title: Read a Dendrogram from a Newick Formatted File
> ### Aliases: ReadDendrogram
> 
> ### ** 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)
   |                                                                               |                                                                      |   0%   |                                                                               |==============================================                        |  66%   |                                                                               |======================================================================| 100%

Time difference of 0.01 secs

> 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
[1] TRUE
> 
> unlink(tf)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>