Nothing
R/plot.phylo2.R
In iteRates: Parametric rate comparison
plot.phylo2 <- function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL,
show.tip.label = TRUE, show.node.label = FALSE, edge.color = "black",
edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
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, ...)
{
nodeHeight<-function(Ntip, Nnode, edge, Nedge, yy){
S <- 0
n <- 0
for (i in 1:(Nedge-1)){
S <- S + yy[edge[i,2]]
n <- n + 1
# cat("\n","n=",n," i=",i," S=",S)
if (edge[i+1,1] != edge[i,1]){
# cat("\n",i,S,n,yy[edge[i,1]],S/n)
yy[edge[i,1]] <- S/n
S <- 0
n <- 0
}
# cat("\n","length of yy",sum(yy!=0))
# cat("\n",yy)
}
S<-S+yy[edge[Nedge,2]]
n<-n+1
yy[edge[Nedge,1]]<-S/n
yy
}
nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge,
edge.length, xx = double(Ntip+Nnode)){
for(i in Nedge:1){
xx[edge[i,2]] <- xx[edge[i,1]]+edge.length[i]
}
xx
}
nodeDepth<-function(Ntip, Nnode, edge, Nedge, xx = double(Ntip+Nnode)){
xx[1:Ntip]<-1
for(i in 1:Nedge){
xx[edge[i,1]] <- xx[edge[i,1]]+xx[edge[i,2]]
}
xx
}
#################################
Ntip <- length(x$tip.label)
if (Ntip == 1) {
warning("found only one tip in the tree")
return(NULL)
}
if (any(tabulate(x$edge[, 1]) == 1))
stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
"unrooted", "radial"))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length))
use.edge.length <- FALSE
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge)
root.edge <- FALSE
if (type == "fan" && root.edge) {
warning("drawing root edge with type = 'fan' is not yet supported")
root.edge <- FALSE
}
phyloORclado <- type %in% c("phylogram", "cladogram")
horizontal <- direction %in% c("rightwards", "leftwards")
xe <- x$edge
if (phyloORclado) {
phyOrder <- attr(x, "order")
if (is.null(phyOrder) || phyOrder != "cladewise") {
x <- reorder(x)
if (!identical(x$edge, xe)) {
ereorder <- match(x$edge[, 2], xe[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
}
}
yy <- numeric(Ntip + Nnode)
TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
z <- reorder(x, order = "pruningwise")
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
if (type == "cladogram" && !use.edge.length)
node.pos <- 2
}
if (node.pos == 1)
yy <- nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
else {
# ans <- .C("node_height_clado", as.integer(Ntip),
# as.integer(Nnode), as.integer(z$edge[, 1]), as.integer(z$edge[,
# 2]), as.integer(Nedge), double(Ntip + Nnode),
# as.double(yy), DUP = FALSE)
# xx <- ans[[6]] - 1
# yy <- ans[[7]]
}
if (!use.edge.length) {
if (node.pos != 2)
xx <- nodeDepth(Ntip, Nnode, z$edge, Nedge) -
1
xx <- max(xx) - xx
}
else {
xx <- nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge,
z$edge.length)
}
}
else {
# rotate.tree <- 2 * pi * rotate.tree/360
switch(type, fan = {
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
xx <- seq(0, 2 * pi * (1 - 1/Ntip), 2 * pi/Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
theta <- nodeHeight(Ntip, Nnode, z$edge, Nedge,
theta)
if (use.edge.length) {
r <- nodeDepthEdgelength(Ntip, Nnode, z$edge,
Nedge, z$edge.length)
} else {
r <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
r <- 1/r
}
theta <- theta
xx <- r * cos(theta)
yy <- r * sin(theta)
}, unrooted = {
nb.sp <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length) unrooted.xy(Ntip, Nnode,
z$edge, z$edge.length, nb.sp) else unrooted.xy(Ntip,
Nnode, z$edge, rep(1, Nedge), nb.sp)
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
}, radial = {
X <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
X[X == 1] <- 0
X <- 1 - X/Ntip
yy <- c((1:Ntip) * 2 * pi/Ntip, rep(0, Nnode))
Y <- nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
# xx <- X * cos(Y + rotate.tree)
# yy <- X * sin(Y + rotate.tree)
})
}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp - min(tmp) + 1
}
if (root.edge) {
if (direction == "rightwards")
xx <- xx + x$root.edge
if (direction == "upwards")
yy <- yy + x$root.edge
}
}
if (no.margin)
par(mai = rep(0, 4))
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
x.lim <- c(0, NA)
pin1 <- par("pin")[1]
strWi <- strwidth(x$tip.label, "inches")
xx.tips <- xx[1:Ntip] * 1.04
alp <- try(uniroot(function(a) max(a * xx.tips +
strWi) - pin1, c(0, 1e+06))$root, silent = TRUE)
if (is.character(alp))
tmp <- max(xx.tips) * 1.5
else {
tmp <- if (show.tip.label)
max(xx.tips + strWi/alp)
else max(xx.tips)
}
x.lim[2] <- tmp
}
else x.lim <- c(1, Ntip)
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
x.lim <- c(min(xx) - offset, max(xx) + offset)
} else x.lim <- c(min(xx), max(xx))
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
}, radial = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
})
}
else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal)
x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
x.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
if (type == "radial")
x.lim[1] <- if (show.tip.label)
-1 - max(nchar(x$tip.label) * 0.03 * cex)
else -1
}
if (phyloORclado && direction == "leftwards")
xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal)
y.lim <- c(1, Ntip)
else {
y.lim <- c(0, NA)
pin2 <- par("pin")[2]
strWi <- strwidth(x$tip.label, "inches")
yy.tips <- yy[1:Ntip] * 1.04
alp <- try(uniroot(function(a) max(a * yy.tips +
strWi) - pin2, c(0, 1e+06))$root, silent = TRUE)
if (is.character(alp))
tmp <- max(yy.tips) * 1.5
else {
tmp <- if (show.tip.label)
max(yy.tips + strWi/alp)
else max(yy.tips)
}
y.lim[2] <- tmp
}
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
}, radial = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
})
}
else if (length(y.lim) == 1) {
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal)
y.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label)
-1 - max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
else -1
}
if (phyloORclado && direction == "downwards")
yy <- max(yy) - yy
if (phyloORclado && root.edge) {
if (direction == "leftwards")
x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards")
y.lim[2] <- y.lim[2] + x$root.edge
}
asp <- if (type %in% c("fan", "radial", "unrooted"))
1
else NA
plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE,
axes = FALSE, asp = asp, ...)
if (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards")
1
else 0
if (phyloORclado && show.tip.label) {
MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 -
adj)
}
if (!horizontal) {
psr <- par("usr")
MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] -
psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot2(x$edge, Ntip, Nnode, xx, yy, horizontal,
edge.color, edge.width, edge.lty)
}
else {
if (type == "fan") {
ereorder <- match(z$edge[, 2], x$edge[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
circular.plot(z$edge, Ntip, Nnode, xx, yy, theta,
r, edge.color, edge.width, edge.lty)
}
else cladogram.plot(x$edge, xx, yy, edge.color, edge.width,
edge.lty)
}
if (root.edge)
switch(direction, rightwards = segments(0, yy[ROOT],
x$root.edge, yy[ROOT]), leftwards = segments(xx[ROOT],
yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT]),
upwards = segments(xx[ROOT], 0, xx[ROOT], x$root.edge),
downwards = segments(xx[ROOT], yy[ROOT], xx[ROOT],
yy[ROOT] + x$root.edge))
if (show.tip.label) {
if (is.expression(x$tip.label))
underscore <- TRUE
if (!underscore)
x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado)
text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label,
adj = adj, font = font, srt = srt, cex = cex,
col = tip.color)
if (type == "unrooted") {
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(XY$axe) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
1.05
sel <- abs(XY$axe) > pi/4 & abs(XY$axe) < 0.75 *
pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
(2 * abs(XY$axe)[sel]/pi - 0.5)
sel <- XY$axe > pi/4 & XY$axe < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel]/2
sel <- XY$axe < -pi/4 & XY$axe > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] *
0.75
text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] +
y.adj * cex, x$tip.label, adj = c(adj, 0),
font = font, srt = srt, cex = cex, col = tip.color)
}
else {
adj <- abs(XY$axe) > pi/2
srt <- 180 * XY$axe/pi
srt[adj] <- srt[adj] - 180
adj <- as.numeric(adj)
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(XY$axe)
yy.tips <- yy.tips + label.offset * sin(XY$axe)
}
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip) text(xx.tips[i], yy.tips[i],
cex = cex[i], x$tip.label[i], adj = adj[i],
font = font[i], srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
angle <- atan2(yy.tips, xx.tips)
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
s <- xx.tips < 0
angle <- angle * 180/pi
angle[s] <- angle[s] + 180
adj <- as.numeric(s)
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip) text(xx.tips[i], yy.tips[i],
x$tip.label[i], font = font[i], cex = cex[i],
srt = angle[i], adj = adj[i], col = tip.color[i])
}
}
if (show.node.label)
text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
x$node.label, adj = adj, font = font, srt = srt,
cex = cex)
}
L <- list(type = type, use.edge.length = use.edge.length,
node.pos = node.pos, show.tip.label = show.tip.label,
show.node.label = show.node.label, font = font, cex = cex,
adj = adj, srt = srt, no.margin = no.margin, label.offset = label.offset,
x.lim = x.lim, y.lim = y.lim, direction = direction,
tip.color = tip.color, Ntip = Ntip, Nnode = Nnode)
iterEnv <- new.env()
assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
invisible(L)
}
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plot.phylo2 <- function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL,
show.tip.label = TRUE, show.node.label = FALSE, edge.color = "black",
edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
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, ...)
{
nodeHeight<-function(Ntip, Nnode, edge, Nedge, yy){
S <- 0
n <- 0
for (i in 1:(Nedge-1)){
S <- S + yy[edge[i,2]]
n <- n + 1
# cat("\n","n=",n," i=",i," S=",S)
if (edge[i+1,1] != edge[i,1]){
# cat("\n",i,S,n,yy[edge[i,1]],S/n)
yy[edge[i,1]] <- S/n
S <- 0
n <- 0
}
# cat("\n","length of yy",sum(yy!=0))
# cat("\n",yy)
}
S<-S+yy[edge[Nedge,2]]
n<-n+1
yy[edge[Nedge,1]]<-S/n
yy
}
nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge,
edge.length, xx = double(Ntip+Nnode)){
for(i in Nedge:1){
xx[edge[i,2]] <- xx[edge[i,1]]+edge.length[i]
}
xx
}
nodeDepth<-function(Ntip, Nnode, edge, Nedge, xx = double(Ntip+Nnode)){
xx[1:Ntip]<-1
for(i in 1:Nedge){
xx[edge[i,1]] <- xx[edge[i,1]]+xx[edge[i,2]]
}
xx
}
#################################
Ntip <- length(x$tip.label)
if (Ntip == 1) {
warning("found only one tip in the tree")
return(NULL)
}
if (any(tabulate(x$edge[, 1]) == 1))
stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
"unrooted", "radial"))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length))
use.edge.length <- FALSE
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge)
root.edge <- FALSE
if (type == "fan" && root.edge) {
warning("drawing root edge with type = 'fan' is not yet supported")
root.edge <- FALSE
}
phyloORclado <- type %in% c("phylogram", "cladogram")
horizontal <- direction %in% c("rightwards", "leftwards")
xe <- x$edge
if (phyloORclado) {
phyOrder <- attr(x, "order")
if (is.null(phyOrder) || phyOrder != "cladewise") {
x <- reorder(x)
if (!identical(x$edge, xe)) {
ereorder <- match(x$edge[, 2], xe[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
}
}
yy <- numeric(Ntip + Nnode)
TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
z <- reorder(x, order = "pruningwise")
if (phyloORclado) {
if (is.null(node.pos)) {
node.pos <- 1
if (type == "cladogram" && !use.edge.length)
node.pos <- 2
}
if (node.pos == 1)
yy <- nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
else {
# ans <- .C("node_height_clado", as.integer(Ntip),
# as.integer(Nnode), as.integer(z$edge[, 1]), as.integer(z$edge[,
# 2]), as.integer(Nedge), double(Ntip + Nnode),
# as.double(yy), DUP = FALSE)
# xx <- ans[[6]] - 1
# yy <- ans[[7]]
}
if (!use.edge.length) {
if (node.pos != 2)
xx <- nodeDepth(Ntip, Nnode, z$edge, Nedge) -
1
xx <- max(xx) - xx
}
else {
xx <- nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge,
z$edge.length)
}
}
else {
# rotate.tree <- 2 * pi * rotate.tree/360
switch(type, fan = {
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
xx <- seq(0, 2 * pi * (1 - 1/Ntip), 2 * pi/Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
theta <- nodeHeight(Ntip, Nnode, z$edge, Nedge,
theta)
if (use.edge.length) {
r <- nodeDepthEdgelength(Ntip, Nnode, z$edge,
Nedge, z$edge.length)
} else {
r <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
r <- 1/r
}
theta <- theta
xx <- r * cos(theta)
yy <- r * sin(theta)
}, unrooted = {
nb.sp <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length) unrooted.xy(Ntip, Nnode,
z$edge, z$edge.length, nb.sp) else unrooted.xy(Ntip,
Nnode, z$edge, rep(1, Nedge), nb.sp)
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
}, radial = {
X <- nodeDepth(Ntip, Nnode, z$edge, Nedge)
X[X == 1] <- 0
X <- 1 - X/Ntip
yy <- c((1:Ntip) * 2 * pi/Ntip, rep(0, Nnode))
Y <- nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
# xx <- X * cos(Y + rotate.tree)
# yy <- X * sin(Y + rotate.tree)
})
}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp - min(tmp) + 1
}
if (root.edge) {
if (direction == "rightwards")
xx <- xx + x$root.edge
if (direction == "upwards")
yy <- yy + x$root.edge
}
}
if (no.margin)
par(mai = rep(0, 4))
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
x.lim <- c(0, NA)
pin1 <- par("pin")[1]
strWi <- strwidth(x$tip.label, "inches")
xx.tips <- xx[1:Ntip] * 1.04
alp <- try(uniroot(function(a) max(a * xx.tips +
strWi) - pin1, c(0, 1e+06))$root, silent = TRUE)
if (is.character(alp))
tmp <- max(xx.tips) * 1.5
else {
tmp <- if (show.tip.label)
max(xx.tips + strWi/alp)
else max(xx.tips)
}
x.lim[2] <- tmp
}
else x.lim <- c(1, Ntip)
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
x.lim <- c(min(xx) - offset, max(xx) + offset)
} else x.lim <- c(min(xx), max(xx))
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
}, radial = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
})
}
else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal)
x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
x.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
if (type == "radial")
x.lim[1] <- if (show.tip.label)
-1 - max(nchar(x$tip.label) * 0.03 * cex)
else -1
}
if (phyloORclado && direction == "leftwards")
xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal)
y.lim <- c(1, Ntip)
else {
y.lim <- c(0, NA)
pin2 <- par("pin")[2]
strWi <- strwidth(x$tip.label, "inches")
yy.tips <- yy[1:Ntip] * 1.04
alp <- try(uniroot(function(a) max(a * yy.tips +
strWi) - pin2, c(0, 1e+06))$root, silent = TRUE)
if (is.character(alp))
tmp <- max(yy.tips) * 1.5
else {
tmp <- if (show.tip.label)
max(yy.tips + strWi/alp)
else max(yy.tips)
}
y.lim[2] <- tmp
}
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
}, radial = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
})
}
else if (length(y.lim) == 1) {
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal)
y.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label)
-1 - max(nchar(x$tip.label) * 0.018 * max(yy) *
cex)
else -1
}
if (phyloORclado && direction == "downwards")
yy <- max(yy) - yy
if (phyloORclado && root.edge) {
if (direction == "leftwards")
x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards")
y.lim[2] <- y.lim[2] + x$root.edge
}
asp <- if (type %in% c("fan", "radial", "unrooted"))
1
else NA
plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE,
axes = FALSE, asp = asp, ...)
if (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards")
1
else 0
if (phyloORclado && show.tip.label) {
MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 -
adj)
}
if (!horizontal) {
psr <- par("usr")
MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] -
psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot2(x$edge, Ntip, Nnode, xx, yy, horizontal,
edge.color, edge.width, edge.lty)
}
else {
if (type == "fan") {
ereorder <- match(z$edge[, 2], x$edge[, 2])
if (length(edge.color) > 1) {
edge.color <- rep(edge.color, length.out = Nedge)
edge.color <- edge.color[ereorder]
}
if (length(edge.width) > 1) {
edge.width <- rep(edge.width, length.out = Nedge)
edge.width <- edge.width[ereorder]
}
if (length(edge.lty) > 1) {
edge.lty <- rep(edge.lty, length.out = Nedge)
edge.lty <- edge.lty[ereorder]
}
circular.plot(z$edge, Ntip, Nnode, xx, yy, theta,
r, edge.color, edge.width, edge.lty)
}
else cladogram.plot(x$edge, xx, yy, edge.color, edge.width,
edge.lty)
}
if (root.edge)
switch(direction, rightwards = segments(0, yy[ROOT],
x$root.edge, yy[ROOT]), leftwards = segments(xx[ROOT],
yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT]),
upwards = segments(xx[ROOT], 0, xx[ROOT], x$root.edge),
downwards = segments(xx[ROOT], yy[ROOT], xx[ROOT],
yy[ROOT] + x$root.edge))
if (show.tip.label) {
if (is.expression(x$tip.label))
underscore <- TRUE
if (!underscore)
x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado)
text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label,
adj = adj, font = font, srt = srt, cex = cex,
col = tip.color)
if (type == "unrooted") {
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(XY$axe) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
1.05
sel <- abs(XY$axe) > pi/4 & abs(XY$axe) < 0.75 *
pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
(2 * abs(XY$axe)[sel]/pi - 0.5)
sel <- XY$axe > pi/4 & XY$axe < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel]/2
sel <- XY$axe < -pi/4 & XY$axe > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] *
0.75
text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] +
y.adj * cex, x$tip.label, adj = c(adj, 0),
font = font, srt = srt, cex = cex, col = tip.color)
}
else {
adj <- abs(XY$axe) > pi/2
srt <- 180 * XY$axe/pi
srt[adj] <- srt[adj] - 180
adj <- as.numeric(adj)
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(XY$axe)
yy.tips <- yy.tips + label.offset * sin(XY$axe)
}
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip) text(xx.tips[i], yy.tips[i],
cex = cex[i], x$tip.label[i], adj = adj[i],
font = font[i], srt = srt[i], col = tip.color[i])
}
}
if (type %in% c("fan", "radial")) {
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
angle <- atan2(yy.tips, xx.tips)
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
s <- xx.tips < 0
angle <- angle * 180/pi
angle[s] <- angle[s] + 180
adj <- as.numeric(s)
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip) text(xx.tips[i], yy.tips[i],
x$tip.label[i], font = font[i], cex = cex[i],
srt = angle[i], adj = adj[i], col = tip.color[i])
}
}
if (show.node.label)
text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
x$node.label, adj = adj, font = font, srt = srt,
cex = cex)
}
L <- list(type = type, use.edge.length = use.edge.length,
node.pos = node.pos, show.tip.label = show.tip.label,
show.node.label = show.node.label, font = font, cex = cex,
adj = adj, srt = srt, no.margin = no.margin, label.offset = label.offset,
x.lim = x.lim, y.lim = y.lim, direction = direction,
tip.color = tip.color, Ntip = Ntip, Nnode = Nnode)
iterEnv <- new.env()
assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
envir = .PlotPhyloEnv)
invisible(L)
}
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