R/plotPhyloUpon.R
In heibl/viper: VIsualitaion of Phylogenetics and Evolution with R
## This code is part of the viper package
## © C. Heibl 2014 (last update 2018-04-04)
#' @title Plot Phylogenies
#' @description Plot phylogenetic trees exactly like \code{\link{plot.phylo}},
#' with one important difference: The plot will be added to existing plots in
#' the graphical device.
#' @importFrom ape unrooted.xy
#' @importFrom stats reorder
#' @importFrom utils globalVariables
#' @export
plotPhyloUpon <- 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 = NULL, tip.color = "black",
plot = TRUE, rotate.tree = 0, open.angle = 0, node.depth = 1,
align.tip.label = FALSE, ...) {
# get parameters from previous plot
# ---------------------------------
# globalVariables(".PlotPhyloEnv")
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
direction <- lastPP$direction
type <- lastPP$type
x.lim <- lastPP$x.lim
## Emmanuel Paradis' code; note comment at lines 311/312!
## ------------------------------------------------------
Ntip <- length(x$tip.label)
if (Ntip < 2) {
warning("found less than 2 tips in the tree")
return(NULL)
}
.nodeHeight <- function(edge, Nedge, yy) .C(node_height,
as.integer(edge[, 1]), as.integer(edge[, 2]), as.integer(Nedge),
as.double(yy))[[4]]
.nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth) .C(node_depth,
as.integer(Ntip), as.integer(edge[, 1]), as.integer(edge[,
2]), as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth))[[5]]
.nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge,
edge.length) .C(node_depth_edgelength, as.integer(edge[,
1]), as.integer(edge[, 2]), as.integer(Nedge), as.double(edge.length),
double(Ntip + Nnode))[[5]]
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
if (any(x$edge < 1) || any(x$edge > Ntip + Nnode))
stop("tree badly conformed; cannot plot. Check the edge matrix.")
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$edge.length)) {
use.edge.length <- FALSE
}
else {
if (use.edge.length && type != "radial") {
tmp <- sum(is.na(x$edge.length))
if (tmp) {
warning(paste(tmp, "branch length(s) NA(s): branch lengths ignored in the plot"))
use.edge.length <- FALSE
}
}
}
if (is.numeric(align.tip.label)) {
align.tip.label.lty <- align.tip.label
align.tip.label <- TRUE
}
else {
if (align.tip.label)
align.tip.label.lty <- 3
}
if (align.tip.label) {
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.ultrametric(x))
align.tip.label <- FALSE
}
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge)
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$edge[, 2] <= Ntip, 2]
yy[TIPS] <- 1:Ntip
}
z <- reorder(x, order = "postorder")
if (phyloORclado) {
if (is.null(node.pos))
node.pos <- if (type == "cladogram" && !use.edge.length)
2
else 1
if (node.pos == 1)
yy <- .nodeHeight(z$edge, Nedge, yy)
else {
ans <- .C(node_height_clado, as.integer(Ntip), as.integer(z$edge[,
1]), as.integer(z$edge[, 2]), as.integer(Nedge),
double(Ntip + Nnode), as.double(yy))
xx <- ans[[5]] - 1
yy <- ans[[6]]
}
if (!use.edge.length) {
if (node.pos != 2)
xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge,
node.depth) - 1
xx <- max(xx) - xx
}
else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge,
z$edge.length)
}
}
else {
twopi <- 2 * pi
rotate.tree <- twopi * rotate.tree/360
if (type != "unrooted") {
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
xx <- seq(0, twopi * (1 - 1/Ntip) - twopi * open.angle/360,
length.out = Ntip)
theta <- double(Ntip)
theta[TIPS] <- xx
theta <- c(theta, numeric(Nnode))
}
switch(type, fan = {
theta <- .nodeHeight(z$edge, Nedge, theta)
if (use.edge.length) {
r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge,
Nedge, z$edge.length)
} else {
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
r <- 1/r
}
theta <- theta + rotate.tree
if (root.edge) r <- r + x$root.edge
xx <- r * cos(theta)
yy <- r * sin(theta)
}, unrooted = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
XY <- if (use.edge.length) unrooted.xy(Ntip, Nnode,
z$edge, z$edge.length, nb.sp, rotate.tree) else unrooted.xy(Ntip,
Nnode, z$edge, rep(1, Nedge), nb.sp, rotate.tree)
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
}, radial = {
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
r[r == 1] <- 0
r <- 1 - r/Ntip
theta <- .nodeHeight(z$edge, Nedge, theta) + rotate.tree
xx <- r * cos(theta)
yy <- r * sin(theta)
})
}
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 (show.tip.label)
nchar.tip.label <- nchar(x$tip.label)
max.yy <- max(yy)
getLimit <- function(x, lab, sin, cex) {
s <- strwidth(lab, "inches", cex = cex)
if (any(s > sin))
return(1.5 * max(x))
Limit <- 0
while (any(x > Limit)) {
i <- which.max(x)
alp <- x[i]/(sin - s[i])
Limit <- x[i] + alp * s[i]
x <- x + alp * s
}
Limit
}
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
xx.tips <- xx[1:Ntip]
if (show.tip.label) {
pin1 <- par("pin")[1]
tmp <- getLimit(xx.tips, x$tip.label, pin1,
cex)
tmp <- tmp + label.offset
}
else tmp <- max(xx.tips)
x.lim <- c(0, tmp)
}
else x.lim <- c(1, Ntip)
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy *
cex)
x.lim <- range(xx) + c(-offset, offset)
} else x.lim <- range(xx)
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar.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.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.tip.label * 0.018 * max.yy *
cex)
if (type == "radial")
x.lim[1] <- if (show.tip.label)
-1 - max(nchar.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 {
pin2 <- par("pin")[2]
yy.tips <- yy[1:Ntip]
if (show.tip.label) {
tmp <- getLimit(yy.tips, x$tip.label, pin2,
cex)
tmp <- tmp + label.offset
}
else tmp <- max(yy.tips)
y.lim <- c(0, tmp)
}
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy *
cex)
y.lim <- c(min(yy) - offset, max.yy + offset)
} else y.lim <- c(min(yy), max.yy)
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy *
cex)
y.lim <- c(0 - offset, max.yy + offset)
} else y.lim <- c(0, max.yy)
}, radial = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
})
}
else if (length(y.lim) == 1) {
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal)
y.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
y.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy *
cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label)
-1 - max(nchar.tip.label * 0.018 * max.yy * cex)
else -1
}
if (phyloORclado && direction == "downwards")
yy <- y.lim[2] - yy
if (phyloORclado && root.edge) {
if (direction == "leftwards")
x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards")
y.lim[2] <- y.lim[2] + x$root.edge
}
asp <- if (type %in% c("fan", "radial", "unrooted"))
1
else NA
# plot.default(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
# ylab = "", axes = FALSE, asp = asp, ...)
if (plot) {
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards")
1
else 0
if (phyloORclado && show.tip.label) {
MAXSTRING <- max(strwidth(x$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.plot(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$edge, xx, yy, edge.color, edge.width,
edge.lty)
}
if (root.edge) {
rootcol <- if (length(edge.color) == 1)
edge.color
else "black"
rootw <- if (length(edge.width) == 1)
edge.width
else 1
rootlty <- if (length(edge.lty) == 1)
edge.lty
else 1
if (type == "fan") {
tmp <- polar2rect(x$root.edge, theta[ROOT])
segments(0, 0, tmp$x, tmp$y, col = rootcol, lwd = rootw,
lty = rootlty)
}
else {
switch(direction, rightwards = segments(0, yy[ROOT],
x$root.edge, yy[ROOT], col = rootcol, lwd = rootw,
lty = rootlty), leftwards = segments(xx[ROOT],
yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT],
col = rootcol, lwd = rootw, lty = rootlty),
upwards = segments(xx[ROOT], 0, xx[ROOT], x$root.edge,
col = rootcol, lwd = rootw, lty = rootlty),
downwards = segments(xx[ROOT], yy[ROOT], xx[ROOT],
yy[ROOT] + x$root.edge, col = rootcol, lwd = rootw,
lty = rootlty))
}
}
if (show.tip.label) {
if (is.expression(x$tip.label))
underscore <- TRUE
if (!underscore)
x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado) {
if (align.tip.label) {
xx.tmp <- switch(direction, rightwards = max(xx[1:Ntip]),
leftwards = min(xx[1:Ntip]), upwards = xx[1:Ntip],
downwards = xx[1:Ntip])
yy.tmp <- switch(direction, rightwards = yy[1:Ntip],
leftwards = yy[1:Ntip], upwards = max(yy[1:Ntip]),
downwards = min(yy[1:Ntip]))
segments(xx[1:Ntip], yy[1:Ntip], xx.tmp, yy.tmp,
lty = align.tip.label.lty)
}
else {
xx.tmp <- xx[1:Ntip]
yy.tmp <- yy[1:Ntip]
}
text(xx.tmp + lox, yy.tmp + loy, x$tip.label,
adj = adj, font = font, srt = srt, cex = cex,
col = tip.color)
}
else {
angle <- if (type == "unrooted")
XY$axe
else atan2(yy[1:Ntip], xx[1:Ntip])
lab4ut <- if (is.null(lab4ut)) {
if (type == "unrooted")
"horizontal"
else "axial"
}
else match.arg(lab4ut, c("horizontal", "axial"))
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(angle) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
1.05
sel <- abs(angle) > pi/4 & abs(angle) < 0.75 *
pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
(2 * abs(angle)[sel]/pi - 0.5)
sel <- angle > pi/4 & angle < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel]/2
sel <- angle < -pi/4 & angle > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] *
0.75
text(xx.tips + x.adj * cex, yy.tips + y.adj *
cex, x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
}
else {
if (align.tip.label) {
POL <- rect2polar(xx.tips, yy.tips)
POL$r[] <- max(POL$r)
REC <- polar2rect(POL$r, POL$angle)
xx.tips <- REC$x
yy.tips <- REC$y
segments(xx[1:Ntip], yy[1:Ntip], xx.tips,
yy.tips, lty = align.tip.label.lty)
}
if (type == "unrooted") {
adj <- abs(angle) > pi/2
angle <- angle * 180/pi
angle[adj] <- angle[adj] - 180
adj <- as.numeric(adj)
}
else {
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, node.depth = node.depth, 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, root.time = x$root.time,
# align.tip.label = align.tip.label)
# assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
# envir = .PlotPhyloEnv)
# invisible(L)
}
heibl/viper documentation built on May 21, 2019, 10:47 a.m.
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## This code is part of the viper package
## © C. Heibl 2014 (last update 2018-04-04)
#' @title Plot Phylogenies
#' @description Plot phylogenetic trees exactly like \code{\link{plot.phylo}},
#' with one important difference: The plot will be added to existing plots in
#' the graphical device.
#' @importFrom ape unrooted.xy
#' @importFrom stats reorder
#' @importFrom utils globalVariables
#' @export
plotPhyloUpon <- function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL,
show.tip.label = TRUE, show.node.label = FALSE, edge.color = "black",
edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE,
label.offset = 0, underscore = FALSE, x.lim = NULL, y.lim = NULL,
direction = "rightwards", lab4ut = NULL, tip.color = "black",
plot = TRUE, rotate.tree = 0, open.angle = 0, node.depth = 1,
align.tip.label = FALSE, ...) {
# get parameters from previous plot
# ---------------------------------
# globalVariables(".PlotPhyloEnv")
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
direction <- lastPP$direction
type <- lastPP$type
x.lim <- lastPP$x.lim
## Emmanuel Paradis' code; note comment at lines 311/312!
## ------------------------------------------------------
Ntip <- length(x$tip.label)
if (Ntip < 2) {
warning("found less than 2 tips in the tree")
return(NULL)
}
.nodeHeight <- function(edge, Nedge, yy) .C(node_height,
as.integer(edge[, 1]), as.integer(edge[, 2]), as.integer(Nedge),
as.double(yy))[[4]]
.nodeDepth <- function(Ntip, Nnode, edge, Nedge, node.depth) .C(node_depth,
as.integer(Ntip), as.integer(edge[, 1]), as.integer(edge[,
2]), as.integer(Nedge), double(Ntip + Nnode), as.integer(node.depth))[[5]]
.nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge,
edge.length) .C(node_depth_edgelength, as.integer(edge[,
1]), as.integer(edge[, 2]), as.integer(Nedge), as.double(edge.length),
double(Ntip + Nnode))[[5]]
Nedge <- dim(x$edge)[1]
Nnode <- x$Nnode
if (any(x$edge < 1) || any(x$edge > Ntip + Nnode))
stop("tree badly conformed; cannot plot. Check the edge matrix.")
ROOT <- Ntip + 1
type <- match.arg(type, c("phylogram", "cladogram", "fan",
"unrooted", "radial"))
direction <- match.arg(direction, c("rightwards", "leftwards",
"upwards", "downwards"))
if (is.null(x$edge.length)) {
use.edge.length <- FALSE
}
else {
if (use.edge.length && type != "radial") {
tmp <- sum(is.na(x$edge.length))
if (tmp) {
warning(paste(tmp, "branch length(s) NA(s): branch lengths ignored in the plot"))
use.edge.length <- FALSE
}
}
}
if (is.numeric(align.tip.label)) {
align.tip.label.lty <- align.tip.label
align.tip.label <- TRUE
}
else {
if (align.tip.label)
align.tip.label.lty <- 3
}
if (align.tip.label) {
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.ultrametric(x))
align.tip.label <- FALSE
}
if (type %in% c("unrooted", "radial") || !use.edge.length ||
is.null(x$root.edge) || !x$root.edge)
root.edge <- FALSE
phyloORclado <- type %in% c("phylogram", "cladogram")
horizontal <- direction %in% c("rightwards", "leftwards")
xe <- x$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 = "postorder")
if (phyloORclado) {
if (is.null(node.pos))
node.pos <- if (type == "cladogram" && !use.edge.length)
2
else 1
if (node.pos == 1)
yy <- .nodeHeight(z$edge, Nedge, yy)
else {
ans <- .C(node_height_clado, as.integer(Ntip), as.integer(z$edge[,
1]), as.integer(z$edge[, 2]), as.integer(Nedge),
double(Ntip + Nnode), as.double(yy))
xx <- ans[[5]] - 1
yy <- ans[[6]]
}
if (!use.edge.length) {
if (node.pos != 2)
xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge,
node.depth) - 1
xx <- max(xx) - xx
}
else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge,
z$edge.length)
}
}
else {
twopi <- 2 * pi
rotate.tree <- twopi * rotate.tree/360
if (type != "unrooted") {
TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
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))
}
switch(type, fan = {
theta <- .nodeHeight(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, node.depth)
r <- 1/r
}
theta <- theta + rotate.tree
if (root.edge) r <- r + x$root.edge
xx <- r * cos(theta)
yy <- r * sin(theta)
}, unrooted = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
XY <- if (use.edge.length) unrooted.xy(Ntip, Nnode,
z$edge, z$edge.length, nb.sp, rotate.tree) else unrooted.xy(Ntip,
Nnode, z$edge, rep(1, Nedge), nb.sp, rotate.tree)
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
}, radial = {
r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge, node.depth)
r[r == 1] <- 0
r <- 1 - r/Ntip
theta <- .nodeHeight(z$edge, Nedge, theta) + rotate.tree
xx <- r * cos(theta)
yy <- r * sin(theta)
})
}
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
yy <- xx
xx <- tmp - min(tmp) + 1
}
if (root.edge) {
if (direction == "rightwards")
xx <- xx + x$root.edge
if (direction == "upwards")
yy <- yy + x$root.edge
}
}
if (no.margin)
par(mai = rep(0, 4))
if (show.tip.label)
nchar.tip.label <- nchar(x$tip.label)
max.yy <- max(yy)
getLimit <- function(x, lab, sin, cex) {
s <- strwidth(lab, "inches", cex = cex)
if (any(s > sin))
return(1.5 * max(x))
Limit <- 0
while (any(x > Limit)) {
i <- which.max(x)
alp <- x[i]/(sin - s[i])
Limit <- x[i] + alp * s[i]
x <- x + alp * s
}
Limit
}
if (is.null(x.lim)) {
if (phyloORclado) {
if (horizontal) {
xx.tips <- xx[1:Ntip]
if (show.tip.label) {
pin1 <- par("pin")[1]
tmp <- getLimit(xx.tips, x$tip.label, pin1,
cex)
tmp <- tmp + label.offset
}
else tmp <- max(xx.tips)
x.lim <- c(0, tmp)
}
else x.lim <- c(1, Ntip)
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy *
cex)
x.lim <- range(xx) + c(-offset, offset)
} else x.lim <- range(xx)
}, unrooted = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.018 * max.yy *
cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
}, radial = {
if (show.tip.label) {
offset <- max(nchar.tip.label * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
})
}
else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal)
x.lim[1] <- 1
if (type %in% c("fan", "unrooted") && show.tip.label)
x.lim[1] <- -max(nchar.tip.label * 0.018 * max.yy *
cex)
if (type == "radial")
x.lim[1] <- if (show.tip.label)
-1 - max(nchar.tip.label * 0.03 * cex)
else -1
}
if (phyloORclado && direction == "leftwards")
xx <- x.lim[2] - xx
if (is.null(y.lim)) {
if (phyloORclado) {
if (horizontal)
y.lim <- c(1, Ntip)
else {
pin2 <- par("pin")[2]
yy.tips <- yy[1:Ntip]
if (show.tip.label) {
tmp <- getLimit(yy.tips, x$tip.label, pin2,
cex)
tmp <- tmp + label.offset
}
else tmp <- max(yy.tips)
y.lim <- c(0, tmp)
}
}
else switch(type, fan = {
if (show.tip.label) {
offset <- max(nchar.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.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.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.tip.label * 0.018 * max.yy *
cex)
if (type == "radial")
y.lim[1] <- if (show.tip.label)
-1 - max(nchar.tip.label * 0.018 * max.yy * cex)
else -1
}
if (phyloORclado && direction == "downwards")
yy <- y.lim[2] - 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.default(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
# ylab = "", 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$tip.label, cex = cex))
loy <- 0
if (direction == "rightwards") {
lox <- label.offset + MAXSTRING * 1.05 * adj
}
if (direction == "leftwards") {
lox <- -label.offset - MAXSTRING * 1.05 * (1 -
adj)
}
if (!horizontal) {
psr <- par("usr")
MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] -
psr[1])
loy <- label.offset + MAXSTRING * 1.05 * adj
lox <- 0
srt <- 90 + srt
if (direction == "downwards") {
loy <- -loy
srt <- 180 + srt
}
}
}
if (type == "phylogram") {
phylogram.plot(x$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) {
rootcol <- if (length(edge.color) == 1)
edge.color
else "black"
rootw <- if (length(edge.width) == 1)
edge.width
else 1
rootlty <- if (length(edge.lty) == 1)
edge.lty
else 1
if (type == "fan") {
tmp <- polar2rect(x$root.edge, theta[ROOT])
segments(0, 0, tmp$x, tmp$y, col = rootcol, lwd = rootw,
lty = rootlty)
}
else {
switch(direction, rightwards = segments(0, yy[ROOT],
x$root.edge, yy[ROOT], col = rootcol, lwd = rootw,
lty = rootlty), leftwards = segments(xx[ROOT],
yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT],
col = rootcol, lwd = rootw, lty = rootlty),
upwards = segments(xx[ROOT], 0, xx[ROOT], x$root.edge,
col = rootcol, lwd = rootw, lty = rootlty),
downwards = segments(xx[ROOT], yy[ROOT], xx[ROOT],
yy[ROOT] + x$root.edge, col = rootcol, lwd = rootw,
lty = rootlty))
}
}
if (show.tip.label) {
if (is.expression(x$tip.label))
underscore <- TRUE
if (!underscore)
x$tip.label <- gsub("_", " ", x$tip.label)
if (phyloORclado) {
if (align.tip.label) {
xx.tmp <- switch(direction, rightwards = max(xx[1:Ntip]),
leftwards = min(xx[1:Ntip]), upwards = xx[1:Ntip],
downwards = xx[1:Ntip])
yy.tmp <- switch(direction, rightwards = yy[1:Ntip],
leftwards = yy[1:Ntip], upwards = max(yy[1:Ntip]),
downwards = min(yy[1:Ntip]))
segments(xx[1:Ntip], yy[1:Ntip], xx.tmp, yy.tmp,
lty = align.tip.label.lty)
}
else {
xx.tmp <- xx[1:Ntip]
yy.tmp <- yy[1:Ntip]
}
text(xx.tmp + lox, yy.tmp + loy, x$tip.label,
adj = adj, font = font, srt = srt, cex = cex,
col = tip.color)
}
else {
angle <- if (type == "unrooted")
XY$axe
else atan2(yy[1:Ntip], xx[1:Ntip])
lab4ut <- if (is.null(lab4ut)) {
if (type == "unrooted")
"horizontal"
else "axial"
}
else match.arg(lab4ut, c("horizontal", "axial"))
xx.tips <- xx[1:Ntip]
yy.tips <- yy[1:Ntip]
if (label.offset) {
xx.tips <- xx.tips + label.offset * cos(angle)
yy.tips <- yy.tips + label.offset * sin(angle)
}
if (lab4ut == "horizontal") {
y.adj <- x.adj <- numeric(Ntip)
sel <- abs(angle) > 0.75 * pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
1.05
sel <- abs(angle) > pi/4 & abs(angle) < 0.75 *
pi
x.adj[sel] <- -strwidth(x$tip.label)[sel] *
(2 * abs(angle)[sel]/pi - 0.5)
sel <- angle > pi/4 & angle < 0.75 * pi
y.adj[sel] <- strheight(x$tip.label)[sel]/2
sel <- angle < -pi/4 & angle > -0.75 * pi
y.adj[sel] <- -strheight(x$tip.label)[sel] *
0.75
text(xx.tips + x.adj * cex, yy.tips + y.adj *
cex, x$tip.label, adj = c(adj, 0), font = font,
srt = srt, cex = cex, col = tip.color)
}
else {
if (align.tip.label) {
POL <- rect2polar(xx.tips, yy.tips)
POL$r[] <- max(POL$r)
REC <- polar2rect(POL$r, POL$angle)
xx.tips <- REC$x
yy.tips <- REC$y
segments(xx[1:Ntip], yy[1:Ntip], xx.tips,
yy.tips, lty = align.tip.label.lty)
}
if (type == "unrooted") {
adj <- abs(angle) > pi/2
angle <- angle * 180/pi
angle[adj] <- angle[adj] - 180
adj <- as.numeric(adj)
}
else {
s <- xx.tips < 0
angle <- angle * 180/pi
angle[s] <- angle[s] + 180
adj <- as.numeric(s)
}
font <- rep(font, length.out = Ntip)
tip.color <- rep(tip.color, length.out = Ntip)
cex <- rep(cex, length.out = Ntip)
for (i in 1:Ntip) text(xx.tips[i], yy.tips[i],
x$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$node.label, adj = adj, font = font, srt = srt,
cex = cex)
}
# L <- list(type = type, use.edge.length = use.edge.length,
# node.pos = node.pos, node.depth = node.depth, show.tip.label = show.tip.label,
# show.node.label = show.node.label, font = font, cex = cex,
# adj = adj, srt = srt, no.margin = no.margin, label.offset = label.offset,
# x.lim = x.lim, y.lim = y.lim, direction = direction,
# tip.color = tip.color, Ntip = Ntip, Nnode = Nnode, root.time = x$root.time,
# align.tip.label = align.tip.label)
# assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
# envir = .PlotPhyloEnv)
# invisible(L)
}
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