1 ## cophyloplot.R (2010-03-18)
3 ## Plots two phylogenetic trees face to
4 ## face with the links between the tips
6 ## Copyright 2008-2010 Damien de Vienne
8 ## This file is part of the R-package `ape'.
9 ## See the file ../COPYING for licensing issues.
12 function(x, y, assoc = NULL, use.edge.length = FALSE, space = 0,
13 length.line = 1, gap = 2, type = "phylogram", rotate = FALSE,
14 col = par("fg"), lwd = par("lwd"), lty = par("lty"),
15 show.tip.label = TRUE, font = 3, ...)
18 assoc <- matrix(ncol = 2)
19 print("No association matrix specified. Links will be omitted.")
22 cat("\n Click on a node to rotate (right click to exit)\n\n")
24 res <- plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
25 space = space, length.line = length.line, gap = gap,
26 type = type, return = TRUE, col = col, lwd=lwd, lty=lty, show.tip.label = show.tip.label,
28 click <- identify(res$c[, 1], res$c[, 2], n = 1)
29 if (click < length(res$a[, 1]) + 1) {
30 if (click > res$N.tip.x)
33 else if (click < length(res$c[, 1]) + 1) {
34 if (click > length(res$a[, 1]) + res$N.tip.y)
35 y <- rotate(y, click - length(res$a[, 1]))
37 plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
38 space = space, length.line = length.line, gap = gap,
39 type = type, return = TRUE, col = col, lwd=lwd, lty=lty, show.tip.label = show.tip.label, font = font)
41 on.exit(print("done"))
43 else plotCophylo2(x, y, assoc = assoc, use.edge.length = use.edge.length,
44 space = space, length.line = length.line, gap = gap,
45 type = type, return = FALSE, col = col, lwd=lwd, lty=lty, show.tip.label = show.tip.label, font = font)
49 function (x, y, assoc = assoc, use.edge.length = use.edge.length,
50 space = space, length.line = length.line, gap = gap,
51 type = type, return = return, col = col, lwd=lwd, lty=lty,
52 show.tip.label = show.tip.label,
56 ###choice of the minimum space between the trees
57 left <- max(nchar(x$tip.label, type = "width")) + length.line
58 right <- max(nchar(y$tip.label, type = "width")) + length.line
59 space.min <- left + right + gap * 2
60 if ((space <= 0) || (space < space.min)) space <- space.min
63 res$N.tip.x <- N.tip.x
64 res$N.tip.y <- N.tip.y
65 a <- plotPhyloCoor(x, use.edge.length = use.edge.length, type = type)
67 b <- plotPhyloCoor(y, use.edge.length = use.edge.length,
68 direction = "leftwards", type = type)
69 ###for the two trees to have the extreme leaves at the same ordinate.
70 a[, 2] <- a[, 2] - min(a[, 2])
71 b[, 2] <- b[, 2] - min(b[, 2])
74 b2[, 1] <- b[1:nrow(b), 1] * (max(a[, 1])/max(b[, 1])) +
76 b2[, 2] <- b[1:nrow(b), 2] * (max(a[, 2])/max(b[, 2]))
78 c <- matrix(ncol = 2, nrow = nrow(a) + nrow(b))
79 c[1:nrow(a), ] <- a[1:nrow(a), ]
80 c[nrow(a) + 1:nrow(b), 1] <- b2[, 1]
81 c[nrow(a) + 1:nrow(b), 2] <- b2[, 2]
83 plot(c, type = "n", xlim = NULL, ylim = NULL, log = "", main = NULL,
84 sub = NULL, xlab = NULL, ylab = NULL, ann = FALSE, axes = FALSE,
86 ###segments for cladograms
87 if (type == "cladogram") {
88 for (i in 1:(nrow(a) - 1)) segments(a[x$edge[i, 1], 1],
89 a[x$edge[i, 1], 2], a[x$edge[i, 2], 1], a[x$edge[i,
91 for (i in 1:(nrow(b) - 1))
92 segments(b2[y$edge[i, 1], 1], b2[y$edge[i, 1], 2],
93 b2[y$edge[i, 2], 1], b2[y$edge[i, 2], 2])
95 ###segments for phylograms
96 if (type == "phylogram") {
97 for (i in (N.tip.x + 1):nrow(a)) {
98 l <- length(x$edge[x$edge[, 1] == i, ][, 1])
100 segments(a[x$edge[x$edge[, 1] == i, ][1, 1],
101 1], a[x$edge[x$edge[, 1] == i, 2], 2][1], a[x$edge[x$edge[,
102 1] == i, ][1, 1], 1], a[x$edge[x$edge[, 1] ==
104 segments(a[x$edge[x$edge[, 1] == i, ][1, 1],
105 1], a[x$edge[x$edge[, 1] == i, 2], 2][j], a[x$edge[x$edge[,
106 1] == i, 2], 1][j], a[x$edge[x$edge[, 1] ==
110 for (i in (N.tip.y + 1):nrow(b)) {
111 l <- length(y$edge[y$edge[, 1] == i, ][, 1])
113 segments(b2[y$edge[y$edge[, 1] == i, ][1, 1],
114 1], b2[y$edge[y$edge[, 1] == i, 2], 2][1],
115 b2[y$edge[y$edge[, 1] == i, ][1, 1], 1], b2[y$edge[y$edge[,
117 segments(b2[y$edge[y$edge[, 1] == i, ][1, 1],
118 1], b2[y$edge[y$edge[, 1] == i, 2], 2][j],
119 b2[y$edge[y$edge[, 1] == i, 2], 1][j], b2[y$edge[y$edge[,
124 if (show.tip.label) {
125 text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4,
126 labels = x$tip.label)
127 text(b2[1:N.tip.y, ], cex = 1, font = font, pos = 2,
128 labels = y$tip.label)
130 ###links between associated taxa. Takes into account the size of the character strings of the taxa names.
133 decx <- array(nrow(assoc))
134 decy <- array(nrow(assoc))
137 if (length(col)==1) colors<-c(rep(col, nrow(assoc)))
138 else if (length(col)>=nrow(assoc)) colors<-col
139 else colors<-c(rep(col, as.integer(nrow(assoc)/length(col))+1))
142 if (length(lwd)==1) lwidths<-c(rep(lwd, nrow(assoc)))
143 else if (length(lwd)>=nrow(assoc)) lwidths<-lwd
144 else lwidths<-c(rep(lwd, as.integer(nrow(assoc)/length(lwd))+1))
147 if (length(lty) == 1) ltype <- c(rep(lty, nrow(assoc)))
148 else if (length(lty) >= nrow(assoc)) ltype <- lty
149 else ltype <- c(rep(lty, as.integer(nrow(assoc)/length(lty))+1))
151 for (i in 1:nrow(assoc)) {
152 if (show.tip.label) {
153 decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == assoc[i, 1]]])
154 decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == assoc[i, 2]]])
156 decx[i] <- decy[i] <- 0
159 segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap,
160 a[lsa[x$tip.label == assoc[i, 1]], 2],
161 a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
162 a[lsa[x$tip.label == assoc[i, 1]], 2],
163 col = colors[i], lwd = lwidths[i], lty = ltype[i])
165 segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap),
166 b2[lsb[y$tip.label == assoc[i, 2]], 2],
167 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
168 b2[lsb[y$tip.label == assoc[i, 2]], 2],
169 col = colors[i], lwd = lwidths[i], lty = ltype[i])
171 segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left,
172 a[lsa[x$tip.label == assoc[i, 1]], 2],
173 b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right),
174 b2[lsb[y$tip.label == assoc[i, 2]], 2],
175 col = colors[i], lwd = lwidths[i], lty = ltype[i])
177 if (return == TRUE) return(res)