-## 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)