Package: ape
Version: 3.0-7
-Date: 2012-11-28
+Date: 2012-12-19
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
o The new function 'where' searches patterns in DNA sequences.
o pic() gains an option 'rescaled.tree = FALSE' to return the tree
- with its branch lengths rescaled for the PICs calculation.
+ with its branch lengths rescaled for the PIC calculation.
+
+ o clustal(), muscle(), and tcoffee() gain an option
+ 'original.ordering = TRUE' to ease the comparisons of
+ alignments.
+
+ o plot.phylo() has a new option, open.angle, used when plotting
+ circular trees.
BUG FIXES
o drop.tip() shuffled node labels on some trees.
+ o axisPhylo() now works correctly with circular trees, and gives a
+ sensible error message when type = "r" or "u".
+
+
+OTHER CHANGES
+
+ o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
+
CHANGES IN APE VERSION 3.0-6
s <- as.integer(length(x))
if (s < p) stop("sequence shorter than the pattern")
ans <- .C("where", x, pat, s, p, integer(s), 0L,
- DUP = FALSE, NAOK = TRUE, PACKAGE = "apex")
+ DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
n <- ans[[6]]
if (n) ans[[5]][seq_len(n)] - p + 2L else integer()
}
-## clustal.R (2012-01-12)
+## clustal.R (2012-11-28)
## Multiple Sequence Alignment with External Applications
clustal <- function(x, pw.gapopen = 10, pw.gapext = 0.1,
gapopen = 10, gapext = 0.2, exec = NULL,
- MoreArgs = "", quiet = TRUE)
+ MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
os <- Sys.info()[1]
if (is.null(exec)) {
opts <- paste(prefix, suffix, sep = "=", collapse = " ")
opts <- paste(opts, MoreArgs)
system(paste(exec, opts), ignore.stdout = quiet)
- read.dna(outf, "clustal")
+ res <- read.dna(outf, "clustal")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}
-muscle <- function(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
+muscle <- function(x, exec = "muscle", MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
if (missing(x)) {
system(exec)
if (quiet) opts <- paste(opts, "-quiet")
opts <- paste(opts, MoreArgs)
system(paste(exec, opts))
- read.dna(outf, "fasta")
+ res <- read.dna(outf, "fasta")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}
-tcoffee <- function(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+tcoffee <- function(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
{
if (missing(x)) {
system(exec)
opts <- paste(inf, MoreArgs)
if (quiet) opts <- paste(opts, "-quiet=nothing")
system(paste(exec, opts))
- read.dna("input_tcoffee.aln", "clustal")
+ res <- read.dna("input_tcoffee.aln", "clustal")
+ if (original.ordering) res <- res[labels(x), ]
+ res
}
}
plotCophylo2 <-
- function (x, y, assoc = assoc, use.edge.length = use.edge.length,
- space = space, length.line = length.line, gap = gap,
- type = type, return = return, col = col, lwd=lwd, lty=lty,
- show.tip.label = show.tip.label,
- font = font, ...)
+ function(x, y, assoc = assoc, use.edge.length = use.edge.length,
+ space = space, length.line = length.line, gap = gap,
+ type = type, return = return, col = col, lwd=lwd, lty=lty,
+ show.tip.label = show.tip.label,
+ font = font, ...)
{
res <- list()
###choice of the minimum space between the trees
-## dist.topo.R (2012-03-13)
+## dist.topo.R (2012-12-12)
## Topological Distances, Tree Bipartitions,
## Consensus Trees, and Bootstrapping Phylogenies
## 'x' is a list of objects of class "phylo" possibly with no class
if (!is.null(attr(x, "TipLabel"))) return(x)
ref <- x[[1]]$tip.label
- if (any(table(ref) != 1))
- stop("some tip labels are duplicated in tree no. 1")
n <- length(ref)
- Ntree <- length(x)
- if (Ntree > 1) {
- for (i in 2:Ntree) {
- label <- x[[i]]$tip.label
- if (!identical(label, ref)) {
- if (length(label) != length(ref))
- stop(paste("tree no.", i, "has a different number of tips"))
- ilab <- match(label, ref)
- ## can use tabulate here because 'ilab' contains integers
- if (any(is.na(ilab)))
- stop(paste("tree no.", i, "has different tip labels"))
-### <FIXME> the test below does not seem useful anymore
-### if (any(tabulate(ilab) > 1))
-### stop(paste("some tip labels are duplicated in tree no.", i))
-### </FIXME>
- ie <- match(1:n, x[[i]]$edge[, 2])
- x[[i]]$edge[ie, 2] <- ilab
- }
- x[[i]]$tip.label <- NULL
+ if (length(unique(ref)) != n)
+ stop("some tip labels are duplicated in tree no. 1")
+
+ ## serious improvement by Joseph W. Brown!
+ relabel <- function (y) {
+ label <- y$tip.label
+ if (!identical(label, ref)) {
+ if (length(label) != length(ref))
+ stop(paste("tree ", y, "has a different number of tips"))
+ ilab <- match(label, ref)
+ if (any(is.na(ilab)))
+ stop(paste("tree ", y, "has different tip labels"))
+ ie <- match(1:n, y$edge[, 2])
+ y$edge[ie, 2] <- ilab
}
+ y$tip.label <- NULL
+ y
}
- x[[1]]$tip.label <- NULL
+ x <- lapply(x, relabel)
attr(x, "TipLabel") <- ref
+ class(x) <- "multiPhylo"
x
}
-## drop.tip.R (2012-11-22)
+## drop.tip.R (2012-11-29)
## Remove Tips in a Phylogenetic Tree
if (is.null(phy$node.label)) rep("NA", length(node2tip))
else phy$node.label[node2tip - Ntip]
}
- if (!is.null(phy$node.label))
- phy$node.label <- phy$node.label[-(node2tip - Ntip)]
+# if (!is.null(phy$node.label))
+# phy$node.label <- phy$node.label[-(node2tip - Ntip)]
phy$tip.label <- c(phy$tip.label, new.tip.label)
}
-## plot.phylo.R (2012-10-20)
+## plot.phylo.R (2012-12-19)
## Plot Phylogenies
adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
label.offset = 0, underscore = FALSE, x.lim = NULL,
y.lim = NULL, direction = "rightwards", lab4ut = "horizontal",
- tip.color = "black", plot = TRUE, rotate.tree = 0, ...)
+ tip.color = "black", plot = TRUE, rotate.tree = 0,
+ open.angle = 0, ...)
{
Ntip <- length(x$tip.label)
if (Ntip < 2) {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
} else {
- rotate.tree <- 2 * pi * rotate.tree/360
+ twopi <- 2 * pi
+ rotate.tree <- twopi * rotate.tree/360
switch(type, "fan" = {
## if the tips are not in the same order in tip.label
## and in edge[, 2], we must reorder the angles: we
## use `xx' to store temporarily the angles
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
- xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
+ xx <- seq(0, twopi * (1 - 1/Ntip) - twopi * open.angle/360,
+ length.out = Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
r <- 1/r
}
theta <- theta + rotate.tree
- xx <- r*cos(theta)
- yy <- r*sin(theta)
+ xx <- r * cos(theta)
+ yy <- r * sin(theta)
}, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length)
## radius:
X <- 1 - X/Ntip
## angle (1st compute the angles for the tips):
- yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
+ yy <- c((1:Ntip)*twopi/Ntip, rep(0, Nnode))
Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
xx <- X * cos(Y + rotate.tree)
yy <- X * sin(Y + rotate.tree)
if (type %in% c("fan", "radial")) {
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
- ## using atan2 considerably facilitates things compared to acos...
angle <- atan2(yy.tips, xx.tips) # in radians
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
-## scales.R (2011-05-31)
+## scales.R (2012-12-19)
## Add a Scale Bar or Axis to a Phylogeny Plot
axisPhylo <- function(side = 1, ...)
{
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
- if (lastPP$type %in% c("phylogram", "cladogram")) {
+ type <- lastPP$type
+
+ if (type == "unrooted")
+ stop("axisPhylo() not available for unrooted plots; try add.scale.bar()")
+ if (type == "radial")
+ stop("axisPhylo() not meaningful for this type of plot")
+
+ if (type %in% c("phylogram", "cladogram")) {
if (lastPP$direction %in% c("rightwards", "leftwards")) {
x <- pretty(lastPP$xx)
if (lastPP$direction == "rightwards") maxi <- max(lastPP$xx)
x <- -x
}
}
+ axis(side = side, at = c(maxi - x), labels = abs(x), ...)
+ } else { # type == "fan"
+ n <- lastPP$Ntip
+ xx <- lastPP$xx[1:n]; yy <- lastPP$yy[1:n]
+ r0 <- max(sqrt(xx^2 + yy^2))
+ firstandlast <- c(1, n)
+ theta0 <- mean(atan2(yy[firstandlast], xx[firstandlast]))
+ x0 <- r0 * cos(theta0); y0 <- r0 * sin(theta0)
+ inc <- diff(pretty(c(0, r0))[1:2])
+ srt <- 360*theta0/(2*pi)
+ coef <- -1
+ if (abs(srt) > 90) {
+ srt <- srt + 180
+ coef <- 1
+ }
+ len <- 0.025 * r0 # the length of tick marks
+ r <- r0
+ while (r > 1e-8) {
+ x <- r * cos(theta0); y <- r * sin(theta0)
+ if (len/r < 1) {
+ ra <- sqrt(len^2 + r^2); thetaa <- theta0 + coef * asin(len/r)
+ xa <- ra * cos(thetaa); ya <- ra * sin(thetaa)
+ segments(xa, ya, x, y)
+ text(xa, ya, r0 - r, srt = srt, adj = c(0.5, 1.1), ...)
+ }
+ r <- r - inc
+ }
+ segments(x, y, x0, y0)
}
- axis(side = side, at = c(maxi - x), labels = abs(x), ...)
}
\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)
+ MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
+muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
+ original.ordering = TRUE)
+tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
+ original.ordering = TRUE)
}
\arguments{
\item{x}{an object of class \code{"DNAbin"}.}
\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.}
+ \item{original.ordering}{a logical specifying whether to return the
+ aligned sequences in the same order than in \code{x}.}
}
\details{
\code{clustal} tries to guess the name of the executable program
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
lab4ut = "horizontal", tip.color = "black", plot = TRUE,
- rotate.tree = 0, ...)
+ rotate.tree = 0, open.angle = 0, ...)
\method{plot}{multiPhylo}(x, layout = 1, ...)
}
\arguments{
\item{layout}{the number of trees to be plotted simultaneously.}
\item{\dots}{further arguments to be passed to \code{plot} or to
\code{plot.phylo}.}
+ \item{open.angle}{if \code{type = "f"}, the angle in degrees left
+ blank. Use a non-zero value if you want to call
+ \code{\link{axisPhylo}} after the tree is plotted.}
}
\description{
These functions plot phylogenetic trees on the current graphical
-\names{where}
+\name{where}
\alias{where}
\title{Find Patterns in DNA Sequences}
\description{
projects / ape.git / commitdiff