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plotting_functions.R
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plotting_functions.R
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# scripts to reproduce the analysis and figures from Garrido-Oter et al., 2018
#
# originally by Ruben Garrido-Oter
# garridoo@mpipz.mpg.de
library(ape)
library(ggplot2)
library(reshape)
library(scales)
library(grid)
library(gridExtra)
colAddAlpha <- function(col, alpha=1) {
x <- as.vector(col2rgb(col)) / 255
return(rgb(x[1], x[2], x[3], alpha))
}
plot_btree <- function(tree, output.file="Rplots.pdf", cex.labels=1, label.offset=5.3,
type="fan", use.edge.length=T, edge.width=1, edge.color="black",
align.labels=T, color.labels="black", color.alg.lines="dark grey",
tips.bg="black", tips.col="black", tips.shape=16, tips.cex=1,
barplots.height=1, barplots.width, barplots.col, barplots=F, barplots.offset=0.025,
margins=c(.1, .1, .1, .1), height=8.27, width=11.7) {
if (grepl(".tiff", output.file)) {
tiff(file=output.file, height=height, width=width)
} else {
pdf(file=output.file, height=height, width=width, useDingbats=F)
}
if (align.labels) {
tip.color <- "transparent"
} else {
tip.color <- color.labels
color.labels <- "transparent"
}
par(mai=margins)
plot.phylo(tree, type=type, tip.color=tip.color, use.edge.length=use.edge.length,
label.offset=label.offset, show.node.label=F, edge.width=edge.width,
cex=cex.labels, edge.color=edge.color)
lastPP <- get("last_plot.phylo", envir=.PlotPhyloEnv)
XX <- lastPP$xx
YY <- lastPP$yy
Ntip <- lastPP$Ntip
xx.tips <- XX[1:Ntip]
yy.tips <- YY[1:Ntip]
# align tip labels
if(type=="fan") {
angle <- atan2(yy.tips, xx.tips)
# xx.labels <- label.offset * cos(angle)
# yy.labels <- label.offset * sin(angle)
xx.labels <- xx.tips + label.offset * cos(angle)
yy.labels <- yy.tips + label.offset * sin(angle)
par(xpd=NA)
sapply(1:length(xx.labels), function(i) lines(c(xx.tips[i], xx.labels[i]),
c(yy.tips[i], yy.labels[i]),
lty=3, col=color.alg.lines,
cex=3))
s <- xx.labels < 0
angle <- angle * 180 / pi
angle[s] <- angle[s] + 180
adj <- rep(0, length(tree$tip.label))
adj[which(xx.labels < 0)] <- 1
# sapply(1:length(tree$tip.label), function(i) text(x=xx.labels[i], y=yy.labels[i],
# labels=tree$tip.label[i],
# srt=angle[i], offset=1, cex=cex.labels,
# adj=adj[i], col=color.labels))
# TODO: plot N rings
# plot ring
if (barplots) {
for (j in 1:dim(barplots.height)[2]) {
for (i in 1:dim(barplots.height)[1]) {
w <- barplots.width
dx <- xx.labels[i]
dy <- yy.labels[i]
theta <- atan(dy/dx)
x1<- dx + (w/2) * cos(pi/2 - theta)
y1<- dy - (w/2) * sin(pi/2 - theta)
x2<- dx - (w/2) * cos(pi/2 - theta)
y2<- dy + (w/2) * sin(pi/2 - theta)
s <- if(dx > 0) .1 else -.1
x3<- s * barplots.height[i, j] * cos(theta) + x2
y3<- s * barplots.height[i, j] * sin(theta) + y2
x4<- s * barplots.height[i, j] * cos(theta) + x1
y4<- s * barplots.height[i, j] * sin(theta) + y1
polygon(c(x1, x2, x3, x4), c(y1, y2, y3, y4),
col=barplots.col[i, j], border="transparent", lwd=.1)
offset <- 0.1
xx.labels[i] <- s * offset * cos(theta) + xx.labels[i]
yy.labels[i] <- s * offset * sin(theta) + yy.labels[i]
}
}
}
} else if(type=="phylogram") {
xx.labels=xx.tips + label.offset
yy.labels=yy.tips + label.offset
sapply(1:length(xx.labels), function(i) lines(c(xx.tips[i], max(xx.tips) + label.offset),
c(yy.tips[i], yy.tips[i]),
lty=1, col=color.alg.lines, lwd=edge.width-0.5))
sapply(1:length(tree$tip.label), function(i) text(x=max(xx.labels)+label.offset, y=yy.labels[i],
labels=tree$tip.label[i],
offset=1, cex=cex.labels,
col=color.labels, adj = c(0,0)))
if (barplots) {
for (i in 1:dim(barplots.height)[2]) {
for (j in 1:dim(barplots.height)[1]) {
w <- barplots.width
x1 <- x2 <- max(xx.labels) + barplots.offset * i + label.offset
x3 <- x4 <- max(xx.labels) + barplots.offset * i + label.offset + as.numeric(barplots.height[j, i])
y1 <- y4 <- yy.tips[j] - w
y2 <- y3 <- yy.tips[j] + w
if (barplots.height[j, i] != 0) {
par(xpd=NA)
polygon(c(x1, x2, x3, x4), c(y1, y2, y3, y4),
col=barplots.col[j, i], border="black", lwd=.5)
}
}
}
}
} else if(type=="unrooted"){
sapply(1:length(tree$tip.label), function(i) text(x=xx.tips[i] + label.offset, y=yy.tips[i],
labels=tree$tip.label[i],
offset=1, cex=cex.labels,
col=color.labels))
}
# plot leaf shapes
for (i in 1:length(xx.tips)) {
points(x=xx.tips[i], y=yy.tips[i],
col=tips.col[i], pch=tips.shape[i],
cex=tips.cex[i], bg=tips.bg[i], lwd=0.25)
}
dev.off()
}
# colors
alpha <- 1
c_yellow <- rgb(255 / 255, 255 / 255, 0 / 255, alpha)
c_blue <- rgb( 0 / 255, 000 / 255, 255 / 255, alpha)
c_orange <- rgb(255 / 255, 69 / 255, 0 / 255, alpha)
c_green <- rgb( 50/ 255, 220 / 255, 50 / 255, alpha)
c_dark_green <- rgb( 50 / 255, 200 / 255, 100 / 255, alpha)
c_very_dark_green <- rgb( 50 / 255, 150 / 255, 100 / 255, alpha)
c_sea_green <- rgb( 46 / 255, 129 / 255, 90 / 255, alpha)
c_black <- rgb( 0 / 255, 0 / 255, 0 / 255, alpha)
c_grey <- rgb(180 / 255, 180 / 255, 180 / 255, alpha)
c_dark_brown <- rgb(101 / 255, 67 / 255, 33 / 255, alpha)
c_red <- rgb(200 / 255, 0 / 255, 0 / 255, alpha)
c_dark_red <- rgb(255 / 255, 130 / 255, 0 / 255, alpha)
# ggplot2 theme
main_theme <- theme(panel.background=element_blank(),
panel.grid=element_blank(),
axis.line.x=element_line(color="black"),
axis.line.y=element_line(color="black"),
axis.ticks=element_line(color="black"),
axis.text=element_text(colour="black", size=10),
legend.position="top",
legend.background=element_blank(),
legend.key=element_blank(),
text=element_text(family="sans"))