1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
|
## comparePhylo.R (2024-02-13)
## Compare Two "phylo" Objects
## Copyright 2018-2024 Emmanuel Paradis, 2021-2024 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
comparePhylo <- function(x, y, plot = FALSE, force.rooted = FALSE,
use.edge.length = FALSE, commons = TRUE,
location = "bottomleft", ...)
{
tree1 <- deparse(substitute(x))
tree2 <- deparse(substitute(y))
res <- list()
msg <- paste("=> Comparing", tree1, "with", tree2)
res$messages <- msg
n1 <- Ntip(x)
n2 <- Ntip(y)
tmp <-
if (n1 == n2)
paste("Both trees have the same number of tips:", n1)
else
paste("Trees have different numbers of tips:", n1, "and", n2)
msg <- c(msg, tmp)
tips1 <- x$tip.label
tips2 <- y$tip.label
tips12 <- match(tips1, tips2)
tips21 <- match(tips2, tips1)
tmp <- is.na(tips12)
if (any(tmp))
msg <- c(msg, paste("Tips in", tree1, "not in", tree2, ":",
paste(tips1[tmp], collapse = ", ")))
tmp2 <- is.na(tips21)
if (any(tmp2))
msg <- c(msg, paste("Tips in", tree2, "not in", tree1, ":",
paste(tips2[tmp2], collapse = ", ")))
sameTips <- FALSE
if (!sum(tmp, tmp2)) {
msg <- c(msg, "Both trees have the same tip labels")
sameTips <- TRUE
}
m1 <- Nnode(x)
m2 <- Nnode(y)
tmp <-
if (m1 == m2)
paste("Both trees have the same number of nodes:", m1)
else
paste("Trees have different numbers of nodes:", m1, "and", m2)
msg <- c(msg, tmp)
rooted1 <- is.rooted(x)
rooted2 <- is.rooted(y)
tmp <- if (rooted1) {
if (rooted2) "Both trees are rooted" else paste(tree1, "is rooted,", tree2, "is unrooted")
} else {
if (rooted2) paste(tree1, "is unrooted,", tree2, "is rooted") else "Both trees are unrooted"
}
msg <- c(msg, tmp)
ultra1 <- ultra2 <- FALSE
if (!is.null(x$edge.length)) ultra1 <- is.ultrametric(x)
if (!is.null(y$edge.length)) ultra2 <- is.ultrametric(y)
tmp <- if (ultra1) {
if (ultra2) "Both trees are ultrametric" else paste(tree1, "is ultrametric,", tree2, "is not")
} else {
if (ultra2) paste(tree1, "is not ultrametric,", tree2, "is ultrametric") else "Both trees are not ultrametric"
}
msg <- c(msg, tmp)
if (rooted1 && rooted2 || force.rooted) {
key1 <- makeNodeLabel(x, "md5sum")$node.label
key2 <- makeNodeLabel(y, "md5sum")$node.label
mk12 <- match(key1, key2)
mk21 <- match(key2, key1)
if (any(tmp <- is.na(mk12))) {
nk <- sum(tmp)
msg <- c(msg, paste(nk, if (nk == 1) "clade" else "clades", "in", tree1, "not in", tree2))
}
if (plot) {
def.par <- par(no.readonly = TRUE)
layout(matrix(1:2, 1, 2))
plot(x, use.edge.length = use.edge.length, main = tree1, ...)
nodelabels(node = which(tmp) + n1, pch = 19, col = "blue", cex = 2)
legend(location, legend = paste("Clade absent in", tree2), pch = 19, col = "blue")
}
if (any(tmp <- is.na(mk21))) {
nk <- sum(tmp)
msg <- c(msg, paste(nk, if (nk == 1) "clade" else "clades", "in", tree2, "not in", tree1))
}
if (plot) {
plot(y, use.edge.length = use.edge.length, main = tree2, ...)
nodelabels(node = which(tmp) + n2, pch = 19, col = "red", cex = 2)
legend(location, legend = paste("Clade absent in", tree1), pch = 19, col = "red")
par(def.par)
}
nodes1 <- which(!is.na(mk12))
nodes2 <- mk12[!is.na(mk12)]
if (ultra1 && ultra2) {
bt1 <- branching.times(x)
bt2 <- branching.times(y)
BT <- data.frame(paste0(bt1[nodes1], " (", nodes1 + n1, ")"),
paste0(bt2[nodes2], " (", nodes2 + n2, ")"))
names(BT) <- c(tree1, tree2)
res$BT <- BT
msg <- c(msg, "Branching times of clades in common between both trees: see ..$BT
(node number in parentheses)")
}
if (!is.null(nl1 <- x$node.label) && !is.null(nl2 <- y$node.label)) {
NODES <- data.frame(paste0(nl1[nodes1], " (", nodes1 + n1, ")"),
paste0(nl2[nodes2], " (", nodes2 + n2, ")"))
names(NODES) <- c(tree1, tree2)
res$NODES <- NODES
msg <- c(msg, "Node labels of clades in common between both trees: see ..$NODES
(node number in parentheses)")
}
}
if (sameTips) {
TR <- .compressTipLabel(c(x, y))
TR <- root(TR, attr(TR, "TipLabel")[1])
pp <- prop.part(TR)
common.splits <- which(attr(pp, "number") == 2L)
ncs <- length(common.splits)
tmp <-
if (ncs)
paste(ncs, if (ncs == 1) "split" else "splits", "in common")
else "No split in common"
msg <- c(msg, tmp)
if (plot) {
def.par <- par(no.readonly = TRUE)
co <- "black"#rgb(0, 0, 1, 0.7)
layout(matrix(1:2, 1, 2))
edgecol1 <- rep("black", Nedge(x))
edgew1 <- rep(1, Nedge(x))
edgecol2 <- rep("black", Nedge(y))
edgew2 <- rep(1, Nedge(y))
if (ncs) {
pp1 <- SHORTwise(prop.part(TR[[1]]))
pp2 <- SHORTwise(prop.part(TR[[2]]))
if (commons) {
k1 <- which(!is.na(match(pp1, pp2)) & lengths(pp1) > 1)
k2 <- which(!is.na(match(pp2, pp1)) & lengths(pp2) > 1)
} else {
k1 <- which(is.na(match(pp1, pp2)) & lengths(pp1) > 1)
k2 <- which(is.na(match(pp2, pp1)) & lengths(pp2) > 1)
}
e1 <- match(k1 + n1, TR[[1]]$edge[, 2])
e2 <- match(k2 + n2, TR[[2]]$edge[, 2])
edgecol1[e1] <- edgecol2[e2] <- co
edgew1[e1] <- edgew2[e2] <- 5
}
text4leg <- if (commons) "Split present in both trees" else "Split specific to each tree"
plot(TR[[1]], "u", use.edge.length = use.edge.length,
edge.color = edgecol1, edge.width = edgew1, main = tree1, ...)
legend(location, legend = text4leg, lty = 1, col = "black", lwd = 5, xpd = NA)
plot(TR[[2]], "u", use.edge.length = use.edge.length,
edge.color = edgecol2, edge.width = edgew2, main = tree2, ...)
par(def.par)
}
}
res$messages <- paste0(msg, ".")
class(res) <- "comparePhylo"
res
}
print.comparePhylo <- function(x, ...)
{
cat(x$messages, sep = "\n")
cat("\n")
x$messages <- class(x) <- NULL
if (length(x)) print.default(x)
}
|
