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## phydataplot.R (2017-10-04)
## Annotate Phylogenies
## Copyright 2014-2017 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
polar2rect <- function(r, angle)
list(x = r * cos(angle), y = r * sin(angle))
rect2polar <- function(x, y)
list(r = sqrt(x^2 + y^2), angle = atan2(y, x))
.matchDataPhylo <- function(x, phy)
{
msg <- "'x' has no (row)names: data are assumed to be in the same order than the tips of the tree"
labs <- phy$tip.label
if (is.vector(x)) { # also for lists
if (is.null(names(x))) warning(msg) else x <- x[labs]
} else {
if (is.null(rownames(x))) warning(msg) else x <- x[labs, ]
}
x
}
ring <- function(x, phy, style = "ring", offset = 1, ...)
{
style <- match.arg(style, c("ring", "segments", "arrows"))
x <- .matchDataPhylo(x, phy)
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
n <- lastPP$Ntip
one2n <- seq_len(n)
tmp <- rect2polar(lastPP$xx[one2n], lastPP$yy[one2n])
theta <- tmp$angle
r0 <- max(tmp$r) + offset
r1 <- r0 + x
s0 <- polar2rect(rep.int(r0, 100L), seq(0, 2*pi, length.out = 100L))
s1 <- polar2rect(r1, theta)
switch(style, ring = {
if (length(x) < n) x <- rep_len(x, n)
dx <- dim(x)
if (is.null(dx)) dim(x) <- dx <- c(n, 1L)
nc <- dx[2]
col <- list(...)$col
if (is.null(col)) col <- "grey"
if (nc == 1) {
col <- rep_len(col, n)
} else {
colvar <- col
col <- rep(col[1], n)
}
iangle <- min(diff(sort(theta)))
iangle2 <- iangle / 2
for (i in one2n) {
R <- rep(r0, 100)
THETA <- seq(theta[i] - iangle2, theta[i] + iangle2, length.out = 100)
xy1 <- polar2rect(R, THETA)
xy2 <- polar2rect(R + x[i, 1], THETA)
polygon(c(xy1$x, rev(xy2$x)), c(xy1$y, rev(xy2$y)), col = col[i], border = NA)
if (nc > 1) {
for (j in 2:nc) {
xy1 <- xy2
xy2 <- polar2rect(R + sum(x[i, 1:j]), THETA)
polygon(c(xy1$x, rev(xy2$x)), c(xy1$y, rev(xy2$y)), col = colvar[j], border = NA)
}
}
}
##polypath(c(s0$x, NA, s0$x), c(s0$y, NA, s1$y), rule = "evenodd",
## border = 1, col = "transparent")
}, segments = {
s0 <- polar2rect(rep.int(r0, n), theta)
segments(s0$x, s0$y, s1$x, s1$y, ...)
}, arrows = {
s0 <- polar2rect(rep.int(r0, n), theta)
fancyarrows(s0$x, s0$y, s1$x, s1$y, ...)
})
}
phydataplot <- function(x, phy, style = "bars", offset = 1, scaling = 1,
continuous = FALSE, width = NULL, legend = "below",
funcol = rainbow, ...)
{
style <- match.arg(style, c("bars", "segments", "image", "arrows", "boxplot", "dotchart", "mosaic"))
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
circular <- if (lastPP$type %in% c("radial", "fan")) TRUE else FALSE
n <- length(phy$tip.label)
one2n <- seq_len(n)
x <- .matchDataPhylo(x, phy)
if (scaling != 1)
x <- if (is.list(x)) lapply(x, "*", scaling) else scaling * x
if (!circular) {
if (lastPP$direction != "rightwards")
stop("for the moment, only rightwards trees are supported")
x0 <- max(lastPP$xx[one2n]) + offset
if (style %in% c("bars", "segments", "arrows")) x1 <- x0 + x
y1 <- lastPP$yy[one2n]
if (style %in% c("bars", "image", "boxplot", "dotchart", "mosaic")) {
o <- order(y1)
x <- if (style == "image") x[o, o] else
if (is.vector(x)) x[o] else x[o, ]
}
} else {
if (style %in% c("image", "boxplot", "dotchart", "mosaic"))
stop(paste(dQuote(style), "not implemented with circular trees"))
}
switch(style, bars = {
if (circular)
stop("style = \"bars\" not implemented with circular trees; see function 'ring'")
if (!is.null(dim(x))) x <- t(x)
barplot(x, width = 1, add = TRUE, horiz = TRUE, offset = x0,
axes = FALSE, axisnames = FALSE, space = c(0.5, rep(0, n - 1)), ...)
px <- pretty(c(0, x))
axis(1, px + x0, labels = px / scaling, line = 1)
}, segments = {
if (circular) ring(x, phy, style, offset, ...)
else segments(x0, y1, x1, y1, ...)
}, image = {
if (inherits(x, "DNAbin"))
stop('object of class "DNAbin" not supported: use type="mosaic"')
x1 <- seq(x0, lastPP$x.lim[2], length.out = n)
image(x1, y1[o], x, add = TRUE, ...)
mtext(phy$tip.label[o], 1, 1, at = x1, font = lastPP$font,
cex = lastPP$cex, col = lastPP$tip.color)
}, arrows = {
if (circular) ring(x, phy, style, offset, ...)
else fancyarrows(rep(x0, length(y1)), y1, x1, y1, ...)
}, boxplot = {
if (is.matrix(x)) x <- t(x)
o <- boxplot(x, plot = FALSE)
mini <- min(o$stats)
maxi <- max(o$stats)
if (length(o$out)) { # in case there is no outlier
mini <- min(o$out, mini)
maxi <- max(o$out, maxi)
}
px <- pretty(c(mini, maxi))
x0 <- x0 - mini
o$stats <- o$stats + x0
o$out <- o$out + x0
bxp(o, horizontal = TRUE, add = TRUE, axes = FALSE, ...)
axis(1, px + x0, labels = px / scaling, line = 1)
}, dotchart = {
mini <- min(x)
maxi <- max(x)
x0 <- x0 - mini
segments(mini + x0, one2n, maxi + x0, one2n, lty = 3, col = "gray")
points(x + x0, 1:n, ...)
px <- pretty(x)
axis(1, px + x0, labels = px / scaling, line = 1)
}, mosaic = {
p <- ncol(x)
if (is.null(p)) p <- 1L
if (is.null(width)) {
x1 <- lastPP$x.lim[2]
width <- (x1 - x0)/p
} else x1 <- x0 + width * p
xx <- seq(x0, x1, width)
xl <- rep(xx[-length(xx)], each = n)
yb <- rep(one2n - 0.5, p)
xr <- xl + width
yt <- yb + 1
if (!is.null(labx <- colnames(x)))
text(xx[-length(xx)] + width/2, max(yt), labx, adj = c(0.5, -0.5), xpd = TRUE)
if (continuous) {
nux <- if (is.logical(continuous)) 10 else continuous
sq <- seq(min(x), max(x), length.out = nux + 1)
x <- .bincode(x, sq, FALSE, TRUE)
lgd <- paste0("[", sq[-length(sq)], "-", sq[-1], ")")
} else {
if (is.raw(x)) x <- toupper(as.character(x)) # for DNAbin objects
nux <- length(ux <- sort(unique.default(x)))
x <- match(x, ux)
lgd <- as.character(ux)
}
co <- funcol(nux)
conames <- names(co)
if (!is.null(conames)) co <- co[lgd]
rect(xl, yb, xr, yt, col = co[x], xpd = TRUE, ...)
legend <- match.arg(legend, c("below", "side", "none"))
if (legend != "none") {
if (legend == "below")
legend((x0 + x1)/2, -yinch(0.1), lgd, pch = 22, pt.bg = co,
pt.cex = 2, bty = "n", xjust = 0.5, yjust = 0.5,
horiz = TRUE, xpd = TRUE)
else legend(x1, n, lgd, pch = 22, pt.bg = co,
pt.cex = 2, bty = "n", yjust = 1, xpd = TRUE)
}
})
}
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