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## ltt.plot.R (2021-03-01)
## Lineages Through Time Plot
## Copyright 2002-2021 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
ltt.plot.coords <- function(phy, backward = TRUE, tol = 1e-6, type = "S")
{
if (!type %in% c("S", "s")) {
stop("argument type be \"S\" or \"s\".")
}
if (has.singles(phy)) phy <- collapse.singles(phy, root.edge = TRUE) # added 2021-03-01
if (is.ultrametric(phy, tol)) {
if (is.binary.phylo(phy)) {
N <- numeric(phy$Nnode + 1)
N[] <- 1
} else {
node.order <- tabulate(phy$edge[, 1])
N <- node.order[-(1:length(phy$tip.label))] - 1
}
bt <- branching.times(phy)
names(bt) <- NULL
o <- order(bt, decreasing = TRUE)
time <- c(-bt[o], 0)
if (!is.binary.phylo(phy)) N <- c(1, N[o])
} else {
if (!is.binary.phylo(phy)) phy <- multi2di(phy)
n <- Ntip(phy)
m <- phy$Nnode
ROOT <- n + 1L
event <- time.event <- numeric(n + m)
time.event[ROOT] <- 0
phy <- reorder(phy)
for (i in 1:nrow(phy$edge))
time.event[phy$edge[i, 2]] <- time.event[phy$edge[i, 1]] + phy$edge.length[i]
present <- max(time.event)
event[1:n] <- -1
event[ROOT:(n + m)] <- 1
## delete the events that are too close to present:
past.event <- present - time.event > tol
event <- event[past.event]
time.event <- time.event[past.event]
## reorder wrt time:
o <- order(time.event)
time.event <- time.event[o]
event <- event[o]
time <- c(time.event - present, 0)
N <- c(1, event)
}
N <- cumsum(N)
if (!is.null(phy$root.edge)) {
time <- c(time[1] - phy$root.edge, time)
N <- c(1, N)
}
if (!backward) time <- time - time[1]
if (type == "s") {
N <- c(N[2:length(N)], N[length(N)])
}
cbind(time, N)
}
ltt.plot <- function(phy, xlab = "Time", ylab = "N",
backward = TRUE, tol = 1e-6, ...)
{
if (!inherits(phy, "phylo"))
stop("object \"phy\" is not of class \"phylo\"")
xy <- ltt.plot.coords(phy, backward, tol, type = "S")
plot.default(xy, xlab = xlab, ylab = ylab, xaxs = "r",
yaxs = "r", type = "S", ...)
}
ltt.lines <- function(phy, backward = TRUE, tol = 1e-6, ...)
{
xy <- ltt.plot.coords(phy, backward, tol, type = "S")
lines(xy, type = "S", ...)
}
mltt.plot <-
function(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
xlab = "Time", ylab = "N", log = "", backward = TRUE, tol = 1e-6)
{
if (inherits(phy, "phylo")) { # if a tree of class "phylo"
TREES <- list(ltt.plot.coords(phy, backward, tol, type = "S"))
names(TREES) <- deparse(substitute(phy))
} else { # a list of trees
TREES <- lapply(phy, ltt.plot.coords, backward = backward, tol = tol, type = "S")
names(TREES) <- names(phy)
if (is.null(names(TREES)))
names(TREES) <-
paste(deparse(substitute(phy)), "-", 1:length(TREES))
}
dts <- list(...)
n <- length(dts)
if (n) {
mc <- as.character(match.call())[-(1:2)]
nms <- mc[1:n]
for (i in 1:n) {
if (inherits(dts[[i]], "phylo")) {
a <- list(ltt.plot.coords(dts[[i]], backward, tol, type = "S"))
names(a) <- nms[i]
} else { # a list of trees
a <- lapply(dts[[i]], ltt.plot.coords, backward = backward, tol = tol, type = "S")
names(a) <- names(dts[[i]])
if (is.null(names(a)))
names(a) <- paste(deparse(substitute(phy)), "-", seq_along(a))
}
TREES <- c(TREES, a)
}
}
n <- length(TREES)
range.each.tree <- sapply(TREES, function(x) range(x[, 1]))
xl <- range(range.each.tree)
yl <- c(1, max(sapply(TREES, function(x) max(x[, 2]))))
## if backward is FALSE, we have to rescale the time scales of each tree:
if (!backward) {
for (i in seq_along(TREES)) {
tmp <- TREES[[i]]
tmp[, 1] <- tmp[, 1] + xl[2] - range.each.tree[2, i]
TREES[[i]] <- tmp
}
}
plot.default(NA, type = "n", xlim = xl, ylim = yl, xaxs = "r",
yaxs = "r", xlab = xlab, ylab = ylab, log = log)
lty <- if (!dlty) rep(1, n) else 1:n
col <- if (!dcol) rep(1, n) else topo.colors(n)
for (i in 1:n)
lines(TREES[[i]], col = col[i], lty = lty[i], type = "S")
if (legend)
legend(xl[1], yl[2], legend = names(TREES),
lty = lty, col = col, bty = "n")
}
ltt.coplot <- function(phy, backward = TRUE, ...)
{
layout(matrix(1:2, 2))
par(mar = c(0, 3, 0.5, 0.5))
o <- plot(phy, root.edge = TRUE, ...)
par(mar = c(3, 3, 0, 0.5))
ltt.plot(phy, xlim = o$x.lim, backward = FALSE, xaxt = "n")
if (backward) axisPhylo() else axis(1)
}
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