-## plot.phylo.R (2012-03-22)
+## plot.phylo.R (2013-01-11)
## Plot Phylogenies
-## Copyright 2002-2012 Emmanuel Paradis
+## Copyright 2002-2013 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
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$tip.label)
- if (Ntip == 1) {
- warning("found only one tip in the tree")
+ if (Ntip < 2) {
+ warning("found less than 2 tips in the tree")
return(NULL)
}
if (any(tabulate(x$edge[, 1]) == 1))
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)
yy <- xx
xx <- tmp
}
- ## un trait vertical à chaque noeud...
+ ## un trait vertical a chaque noeud...
x0v <- xx[nodes]
y0v <- y1v <- numeric(Nnode)
## store the index of each node in the 1st column of edge:
as.integer(N), double(n + m), DUP = FALSE, PACKAGE = "ape")[[6]]
}
+node.depth.edgelength <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+ .C("node_depth_edgelength", as.integer(n), as.integer(n),
+ as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
+ as.integer(N), as.double(phy$edge.length), double(n + m),
+ DUP = FALSE, PACKAGE = "ape")[[7]]
+}
+
+node.height <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+
+ e1 <- phy$edge[, 1]
+ e2 <- phy$edge[, 2]
+
+ yy <- numeric(n + m)
+ TIPS <- e2[e2 <= n]
+ yy[TIPS] <- 1:n
+
+ .C("node_height", as.integer(n), as.integer(m),
+ as.integer(e1), as.integer(e2), as.integer(N),
+ as.double(yy), DUP = FALSE, PACKAGE = "ape")[[6]]
+}
+
+node.height.clado <- function(phy)
+{
+ n <- length(phy$tip.label)
+ m <- phy$Nnode
+ N <- dim(phy$edge)[1]
+ phy <- reorder(phy, order = "pruningwise")
+
+ e1 <- phy$edge[, 1]
+ e2 <- phy$edge[, 2]
+
+ yy <- numeric(n + m)
+ TIPS <- e2[e2 <= n]
+ yy[TIPS] <- 1:n
+
+ .C("node_height_clado", as.integer(n), as.integer(m),
+ as.integer(e1), as.integer(e2), as.integer(N),
+ double(n + m), as.double(yy), DUP = FALSE,
+ PACKAGE = "ape")[[7]]
+}
+
plot.multiPhylo <- function(x, layout = 1, ...)
{
- if (layout > 1)
- layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
- else layout(matrix(1))
- if (!par("ask")) {
- par(ask = TRUE)
- on.exit(par(ask = FALSE))
+ layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
+ if (!devAskNewPage() && interactive()) {
+ devAskNewPage(TRUE)
+ on.exit(devAskNewPage(FALSE))
}
for (i in 1:length(x)) plot(x[[i]], ...)
}
h <- 1
}
layout(matrix(1:layout, nrow), widths = w, heights = h)
- if (layout > Ntree && !par("ask")) {
- par(ask = TRUE)
- on.exit(par(ask = FALSE))
+ if (layout < Ntree && !devAskNewPage() && interactive()) {
+ devAskNewPage(TRUE)
+ on.exit(devAskNewPage(FALSE))
}
if (horiz) {
for (i in 1:Ntree)