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
171
|
\name{nodelabels}
\alias{nodelabels}
\alias{tiplabels}
\alias{edgelabels}
\title{Labelling the Nodes, Tips, and Edges of a Tree}
\description{
These functions add labels to or near the nodes, the tips, or the
edges of a tree using text or plotting symbols. The text can be
framed.
}
\usage{
nodelabels(text, node, adj = c(0.5, 0.5), frame = "rect",
pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
col = "black", bg = "lightblue", horiz = FALSE,
width = NULL, height = NULL, ...)
tiplabels(text, tip, adj = c(0.5, 0.5), frame = "rect",
pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
col = "black", bg = "yellow", horiz = FALSE,
width = NULL, height = NULL, offset = 0, ...)
edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect",
pch = NULL, thermo = NULL, pie = NULL, piecol = NULL,
col = "black", bg = "lightgreen", horiz = FALSE,
width = NULL, height = NULL, date = NULL, ...)
}
\arguments{
\item{text}{a vector of mode character giving the text to be
printed. Can be left empty.}
\item{node}{a vector of mode numeric giving the numbers of the nodes
where the text or the symbols are to be printed. Can be left empty.}
\item{tip}{a vector of mode numeric giving the numbers of the tips
where the text or the symbols are to be printed. Can be left empty.}
\item{edge}{a vector of mode numeric giving the numbers of the edges
where the text or the symbols are to be printed. Can be left empty.}
\item{adj}{one or two numeric values specifying the horizontal and
vertical, respectively, justification of the text or symbols. By
default, the text is centered horizontally and vertically. If a
single value is given, this alters only the horizontal position of
the text.}
\item{frame}{a character string specifying the kind of frame to be
printed around the text. This must be one of "rect" (the default),
"circle", "none", or any unambiguous abbreviation of these.}
\item{pch}{a numeric giving the type of plotting symbol to be used;
this is eventually recycled. See \code{\link[graphics]{par}} for R's
plotting symbols. If \code{pch} is used, then \code{text} is
ignored.}
\item{thermo}{a numeric vector giving some proportions (values between
0 and 1) for each node, or a numeric matrix giving some proportions
(the rows must sum to one). It can be a data frame which is then
converted into a matrix.}
\item{pie}{same than \code{thermo}.}
\item{piecol}{a list of colours (given as a character vector) to be
used by \code{thermo} or \code{pie}; if left \code{NULL}, a series
of colours given by the function \code{rainbow} is used.}
\item{col}{a character string giving the color to be used for the
text or the plotting symbols; this is eventually recycled.}
\item{bg}{a character string giving the color to be used for the
background of the text frames or of the plotting symbols if it
applies; this is eventually recycled.}
\item{\dots}{further arguments passed to the \code{text} or
\code{points} functions (e.g. \code{cex} to alter the size of the
text or the symbols, or \code{font} for the text; see the examples
below).}
\item{horiz, width, height}{parameters controlling the aspect of
thermometers; by default, their width and height are determined
automatically.}
\item{offset}{offset of the tip labels (can be negative).}
\item{date}{specifies the positions of labels on edges of chronograms
with respect to the time scale.}
}
\details{
These three functions have the same optional arguments and the same
functioning.
If the arguments \code{text} is missing and \code{pch} and
\code{thermo} are left as \code{NULL}, then the numbers of the nodes
(or of the tips) are printed.
If \code{node}, \code{tip}, or \code{edge} is missing, then the text
or the symbols are printed on all nodes, tips, or edges.
The option \code{cex} can be used to change the size of all types of
labels.
A simple call of these functions with no arguments (e.g.,
\code{nodelabels()}) prints the numbers of all nodes (or tips).
In the case of \code{tiplabels}, it would be useful to play with the
options \code{x.lim} and \code{label.offset} (and possibly
\code{show.tip.label}) of \code{plot.phylo} in most cases (see the
examples).
}
\author{Emmanuel Paradis, Ben Bolker, and Jim Lemon}
\seealso{
\code{\link{plot.phylo}}, \code{\link{edges}},
\code{\link{mixedFontLabel}}
}
\examples{
tr <- read.tree(text = "((Homo,Pan),Gorilla);")
plot(tr)
nodelabels("7.3 Ma", 4, frame = "r", bg = "yellow", adj = 0)
nodelabels("5.4 Ma", 5, frame = "c", bg = "tomato", font = 3)
## A trick by Liam Revell when there are many categories:
plot(tr, x.lim = c(-1, 4))
nodelabels(node = 4, pie = matrix(rep(1, 100), 1), cex = 5)
op <- par(fg = "transparent")
nodelabels(node = 5, pie = matrix(rep(1, 100), 1), cex = 5)
par(op)
data(bird.orders)
plot(bird.orders, use.edge.length = FALSE, font = 1)
bs <- round(runif(22, 90, 100), 0) # some imaginary bootstrap values
bs2 <- round(runif(22, 90, 100), 0)
bs3 <- round(runif(22, 90, 100), 0)
nodelabels(bs, adj = 1.2)
nodelabels(bs2, adj = -0.2, bg = "yellow")
### something more classical
plot(bird.orders, use.edge.length = FALSE, font = 1)
nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8)
nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8)
nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)
### the same but we play with the font
plot(bird.orders, use.edge.length = FALSE, font = 1)
nodelabels(bs, adj = -0.2, frame = "n", cex = 0.8, font = 2)
nodelabels(bs2, adj = c(1.2, 1), frame = "n", cex = 0.8, font = 3)
nodelabels(bs3, adj = c(1.2, -0.2), frame = "n", cex = 0.8)
plot(bird.orders, "c", use.edge.length = FALSE, font = 1)
nodelabels(thermo = runif(22), cex = .8)
plot(bird.orders, "u", FALSE, font = 1, lab4ut = "a")
nodelabels(cex = .75, bg = "yellow")
### representing two characters at the tips (you could have as many
### as you want)
plot(bird.orders, "c", FALSE, font = 1, label.offset = 3,
x.lim = 31, no.margin = TRUE)
tiplabels(pch = 21, bg = gray(1:23/23), cex = 2, adj = 1.4)
tiplabels(pch = 19, col = c("yellow", "red", "blue"), adj = 2.5, cex = 2)
### This can be used to highlight tip labels:
plot(bird.orders, font = 1)
i <- c(1, 7, 18)
tiplabels(bird.orders$tip.label[i], i, adj = 0)
### Some random data to compare piecharts and thermometres:
tr <- rtree(15)
x <- runif(14, 0, 0.33)
y <- runif(14, 0, 0.33)
z <- runif(14, 0, 0.33)
x <- cbind(x, y, z, 1 - x - y - z)
layout(matrix(1:2, 1, 2))
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(pie = x, cex = 1.3)
text(4.5, 15, "Are you \"pie\"...", font = 4, cex = 1.5)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
text(4.5, 15, "... or \"thermo\"?", font = 4, cex = 1.5)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), cex = 1.3)
plot(tr, "c", FALSE, no.margin = TRUE)
nodelabels(thermo = x, col = rainbow(4), width = 3, horiz = TRUE)
layout(1)
plot(tr, main = "Showing Edge Lengths")
edgelabels(round(tr$edge.length, 3), srt = 90)
plot(tr, "p", FALSE)
edgelabels("above", adj = c(0.5, -0.25), bg = "yellow")
edgelabels("below", adj = c(0.5, 1.25), bg = "lightblue")
}
\keyword{aplot}
|
