o There is a new image() method for "DNAbin" objects: it plots DNA
alignments in a flexible and efficient way.
+ o Two new functions as.network.phylo and as.igraph.phylo convert
+ trees of class "phylo" into these respective network classes
+ defined in the packages of the same names.
+
+ o The three new functions clustal, muscle, and tcoffee perform
+ nucleotide sequence alignment by calling the external programs
+ of the same names.
+
o base.freq() gains an option 'all' to count all the possible bases
including the ambiguous ones (defaults to FALSE).
- o read.nexus() now writes tree names in the NEXUS file if given a list
- of trees with names.
+ o read.nexus() now writes tree names in the NEXUS file if given a
+ list of trees with names.
BUG FIXES
-## DNA.R (2011-03-15)
+## DNA.R (2011-03-16)
## Manipulations and Comparisons of DNA Sequences
-## as.phylo.R (2010-12-15)
+## as.phylo.R (2011-03-16)
## Conversion Among Tree Objects
-## Copyright 2005-2010 Emmanuel Paradis
+## Copyright 2005-2011 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
class(obj) <- "hclust"
obj
}
+
+as.network.phylo <- function(x, directed = is.rooted(x), ...)
+{
+ if (is.null(x$node.label)) x <- makeNodeLabel(x)
+ res <- network(x$edge, directed = directed, ...)
+ network.vertex.names(res) <- c(x$tip.label, x$node.label)
+ res
+}
+
+as.igraph <- function(x, ...) UseMethod("as.igraph")
+
+as.igraph.phylo <- function(x, directed = is.rooted(x), use.labels = TRUE, ...)
+{
+ ## local copy because x will be changed before evaluating is.rooted(x):
+ directed <- directed
+ if (use.labels) {
+ if (is.null(x$node.label)) x <- makeNodeLabel(x)
+ x$edge <- matrix(c(x$tip.label, x$node.label)[x$edge], ncol = 2)
+ } else x$edge <- x$edge - 1L
+ graph.edgelist(x$edge, directed = directed, ...)
+}
--- /dev/null
+## clustal.R (2011-03-16)
+
+## Multiple Sequence Alignment with External Applications
+
+## Copyright 2011 Emmanuel Paradis
+
+## This file is part of the R-package `ape'.
+## See the file ../COPYING for licensing issues.
+
+clustal <- function(x, pw.gapopen = 10, pw.gapext = 0.1,
+ gapopen = 10, gapext = 0.2, exec = NULL,
+ MoreArgs = "", quiet = TRUE)
+{
+ os <- Sys.info()[1]
+ if (is.null(exec)) {
+ if (os == "Linux") exec <- "clustalw"
+ if (os == "Darwin") exec <- "clustalw2"
+ if (os == "Windows") exec <- "C:/Program Files/ClustalW2/clustalw2"
+ }
+
+ if (missing(x)) {
+ system(paste(exec, "-help"))
+ return(invisible(NULL))
+ }
+
+ d <- tempdir()
+ inf <- paste(d, "input_clustal.fas", sep = "/")
+ outf <- paste(d, "input_clustal.aln", sep = "/")
+ write.dna(x, inf, "fasta")
+ prefix <- c("-INFILE", "-PWGAPOPEN", "-PWGAPEXT", "-GAPOPEN", "-GAPEXT")
+ suffix <- c(inf, pw.gapopen, pw.gapext, gapopen, gapext)
+ opts <- paste(prefix, suffix, sep = "=", collapse = " ")
+ opts <- paste(opts, MoreArgs)
+ system(paste(exec, opts), ignore.stdout = quiet)
+ read.dna(outf, "clustal")
+}
+
+muscle <- function(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
+{
+ if (missing(x)) {
+ system(exec)
+ return(invisible(NULL))
+ }
+
+ d <- tempdir()
+ inf <- paste(d, "input_muscle.fas", sep = "/")
+ outf <- paste(d, "output_muscle.fas", sep = "/")
+ write.dna(x, inf, "fasta")
+ opts <- paste("-in", inf, "-out", outf)
+ if (quiet) opts <- paste(opts, "-quiet")
+ opts <- paste(opts, MoreArgs)
+ system(paste(exec, opts))
+ read.dna(outf, "fasta")
+}
+
+tcoffee <- function(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+{
+ if (missing(x)) {
+ system(exec)
+ return(invisible(NULL))
+ }
+
+ d <- tempdir()
+ od <- setwd(d)
+ on.exit(setwd(od))
+ inf <- "input_tcoffee.fas"
+ write.dna(x, inf, "fasta")
+ opts <- paste(inf, MoreArgs)
+ if (quiet) opts <- paste(opts, "-quiet=nothing")
+ system(paste(exec, opts))
+ read.dna("input_tcoffee.aln", "clustal")
+}
\alias{as.hclust.phylo}
\alias{old2new.phylo}
\alias{new2old.phylo}
-\title{Conversion Among Tree Objects}
+\alias{as.network.phylo}
+\alias{as.igraph}
+\alias{as.igraph.phylo}
+\title{Conversion Among Tree and Network Objects}
+\description{
+ \code{as.phylo} is a generic function which converts an object into a
+ tree of class \code{"phylo"}. There are currently two methods for
+ objects of class \code{"hclust"} and of class \code{"phylog"}
+ (implemented in the package ade4).
+
+ \code{as.hclust.phylo} is a method of the generic
+ \code{\link[stats]{as.hclust}} which converts an object of class
+ \code{"phylo"} into one of class \code{"hclust"}. This can used to
+ convert an object of class \code{"phylo"} into one of class
+ \code{"dendrogram"} (see examples).
+
+ \code{as.network} and \code{as.igraph} convert trees of class
+ \code{"phylo"} into these respective classes defined in the packages
+ of the same names. Note that the generic of the former is defined in
+ \pkg{network}.
+
+ \code{old2new.phylo} and \code{new2old.phylo} are utility functions
+ for converting between the old and new coding of the class
+ \code{"phylo"}.
+}
\usage{
as.phylo(x, ...)
\method{as.phylo}{hclust}(x, ...)
\method{as.hclust}{phylo}(x, ...)
old2new.phylo(phy)
new2old.phylo(phy)
+\method{as.network}{phylo}(x, directed = is.rooted(x), ...)
+as.igraph(x, ...)
+\method{as.igraph}{phylo}(x, directed = is.rooted(x), use.labels = TRUE, ...)
}
\arguments{
\item{x}{an object to be converted into another class.}
+ \item{directed}{a logical value: should the network be directed? By
+ default, this depends on whether the tree is rooted or not.}
+ \item{use.labels}{a logical specifying whether to use labels to build
+ the network of class \code{"igraph"}. If \code{TRUE} and the tree
+ has no node labels, then some default labels are created first. If
+ \code{FALSE}, the network is built with integers.}
\item{\dots}{further arguments to be passed to or from other methods.}
\item{phy}{an object of class \code{"phylo"}.}
}
-\description{
- \code{as.phylo} is a generic function which converts an object into a
- tree of class \code{"phylo"}. There are currently two methods for this
- generic for objects of class \code{"hclust"} and of class
- \code{"phylog"} (implemented in the package ade4).
- \code{as.hclust.phylo} is a method of the generic
- \code{\link[stats]{as.hclust}} which converts an object of class
- \code{"phylo"} into one of class \code{"hclust"}. This can used to
- convert an object of class \code{"phylo"} into one of class
- \code{"dendrogram"} (see examples).
-
- \code{old2new.phylo} and \code{new2old.phylo} are utility functions
- for converting between the old and new coding of the class
- \code{"phylo"}.
-}
\value{
- An object of class \code{"hclust"} or \code{"phylo"}.
+ An object of class \code{"hclust"}, \code{"phylo"}, \code{"network"},
+ or \code{"igraph"}.
}
\author{Emmanuel Paradis}
\seealso{
layout(matrix(1:2, 2, 1))
plot(bird.orders, font = 1, no.margin = TRUE)
par(mar = c(0, 0, 0, 8))
-plot((dend), horiz = TRUE)
+plot(dend, horiz = TRUE)
layout(matrix(1, 1, 1))
+
+### convert into networks:
+if (require(network)) {
+ x <- as.network(rtree(10))
+ print(x)
+ plot(x, vertex.cex = 1:4)
+ plot(x, displaylabels = TRUE)
+}
+tr <- rtree(5)
+if (require(igraph)) {
+ print((x <- as.igraph(tr)))
+ plot(x)
+ print(as.igraph(tr, TRUE, FALSE))
+ print(as.igraph(tr, FALSE, FALSE))
+}
}
\keyword{manip}
--- /dev/null
+\name{clustal}
+\alias{clustal}
+\alias{muscle}
+\alias{tcoffee}
+\title{Multiple Sequence Alignment with External Applications}
+\description{
+ These functions call their respective program from \R to align a set of
+ nucleotide sequences of class \code{"DNAbin"}.
+}
+\usage{
+clustal(x, pw.gapopen = 10, pw.gapext = 0.1,
+ gapopen = 10, gapext = 0.2, exec = NULL,
+ MoreArgs = "", quiet = TRUE)
+muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
+tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+}
+\arguments{
+ \item{x}{an object of class \code{"DNAbin"}.}
+ \item{pw.gapopen, pw.gapext}{gap opening and gap extension penalties
+ used by Clustal during pairwise alignments.}
+ \item{gapopen, gapext}{idem for global alignment.}
+ \item{exec}{a character string giving the name of the program, with
+ its path if necessary. \code{clustal} tries to guess it depending on
+ the operating system (see details).}
+ \item{MoreArgs}{a character string giving additional options.}
+ \item{quiet}{a logical: the default is to not print on \R's console the
+ messages from the external program.}
+}
+\details{
+ \code{clustal} tries to guess the name of the executable program
+ depending on the operating system. Specifically, the followings are
+ used: ``clustalw'' under Linux, ``clustalw2'' under MacOS, or
+ ``C:/Program Files/ClustalW2/clustalw2'' under Windows.
+
+ The calculations are done in a temporary directory which is deleted
+ when \R is quit. So it is possible to find the files created by the
+ last call in the directory printed by \code{tempdir()}.
+
+ When called without arguments (i.e., \code{clustal()}, \dots), the
+ function prints the options of the program which may be passed to
+ \code{MoreArgs}.
+}
+\value{
+ an object of class \code{"DNAbin"} with the aligned sequences.
+}
+\references{
+ Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J.,
+ Higgins, D. G. and Thompson, J. D. (2003) Multiple sequence alignment
+ with the Clustal series of programs. \emph{Nucleic Acids Research}
+ \bold{31}, 3497--3500.
+
+ \url{http://www.clustal.org/}
+
+ Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high
+ accuracy and high throughput. \emph{Nucleic Acids Research},
+ \bold{32}, 1792--1797.
+
+ \url{http://www.drive5.com/muscle/muscle_userguide3.8.html}
+
+ Notredame, C., Higgins, D. and Heringa, J. (2000) T-Coffee: A novel
+ method for multiple sequence alignments. \emph{Journal of Molecular
+ Biology}, \bold{302}, 205--217.
+
+ \url{http://www.tcoffee.org/Documentation/t_coffee/t_coffee_technical.htm}
+}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link{image.DNAbin}}, \code{\link{del.gaps}}
+
+ The package \pkg{phyloch} which has similar functions for the MAFFT
+ and Prank.
+}
+\examples{
+\dontrun{
+### display the options:
+clustal()
+muscle()
+tcoffee()
+
+data(woodmouse)
+### open gaps more easily:
+clustal(woodmouse, pw.gapopen = 1, pw.gapext = 1)
+### T-Coffee requires negative values (quite slow; muscle is much faster):
+tcoffee(woodmouse, MoreArgs = "-gapopen=-10 -gapext=-2")
+}}
+\keyword{manip}
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{DNAbin}}, \code{\link{del.gaps}}, \code{\link{clustal}}
+ \code{\link{DNAbin}}, \code{\link{del.gaps}}, \code{\link{clustal}},
+ \code{\link[graphics]{grid}}
}
\examples{
data(woodmouse)
par(mfcol = c(1, 1))
### zoom on a portion of the data:
image(woodmouse[11:15, 1:50], c("a", "n"), c("blue", "grey"))
+grid(50, 5, col = "black")
### see the guanines on a black background:
image(woodmouse, "g", "yellow", "black")
}
projects / ape.git / commitdiff