Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/WriteDendrogram.R
Writes a dendrogram object to a file in Newick (also known as New Hampshire) parenthetic format.
1 2 3 4 5 6 7 |
x |
An object of class |
file |
A connection or a character string naming the file path where the tree should be exported. If "" (the default), the tree is printed to the standard output connection, the console unless redirected by sink. |
quoteLabels |
Logical specifying whether to place leaf labels in double quotes. |
convertBlanks |
Logical specifying whether to convert spaces in leaf labels to underscores. |
internalLabels |
Logical indicating whether to write any “edgetext” preceding a node as an internal node label. |
digits |
The maximum number of digits to print for edge lengths. |
append |
Logical indicating whether to append to an existing |
WriteDendrogram
will write a dendrogram object to a file
in standard Newick format. Note that special characters (commas, square brackets, colons, semi-colons, and parentheses) present in leaf labels will likely cause a broken Newick file unless quoteLabels
is TRUE
(the default).
NULL
.
Erik Wright eswright@pitt.edu
1 2 3 4 5 | dists <- matrix(c(0, 10, 20, 10, 0, 5, 20, 5, 0),
nrow=3,
dimnames=list(c("dog", "elephant", "horse")))
dend <- IdClusters(dists, method="NJ", type="dendrogram")
WriteDendrogram(dend)
|
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 0.14 secs
("dog":10,("horse":7.5,"elephant":2.5):2.5);
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