3 \alias{plot.multiPhylo}
4 \title{Plot Phylogenies}
6 \method{plot}{phylo}(x, type = "phylogram", use.edge.length = TRUE,
7 node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE,
8 edge.color = "black", edge.width = 1, edge.lty = 1, font = 3,
9 cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
10 root.edge = FALSE, label.offset = 0, underscore = FALSE,
11 x.lim = NULL, y.lim = NULL, direction = "rightwards",
12 lab4ut = "horizontal", tip.color = "black", ...)
13 \method{plot}{multiPhylo}(x, layout = 1, ...)
16 \item{x}{an object of class \code{"phylo"} or of class
18 \item{type}{a character string specifying the type of phylogeny to be
19 drawn; it must be one of "phylogram" (the default), "cladogram",
20 "fan", "unrooted", "radial" or any unambiguous abbreviation of
22 \item{use.edge.length}{a logical indicating whether to use the edge
23 lengths of the phylogeny to draw the branches (the default) or not
24 (if \code{FALSE}). This option has no effect if the object of class
25 \code{"phylo"} has no `edge.length' element.}
26 \item{node.pos}{a numeric taking the value 1 or 2 which specifies the
27 vertical position of the nodes with respect to their descendants. If
28 \code{NULL} (the default), then the value is determined in relation
29 to `type' and `use.edge.length' (see details).}
30 \item{show.tip.label}{a logical indicating whether to show the tip
31 labels on the phylogeny (defaults to \code{TRUE}, i.e. the labels
33 \item{show.node.label}{a logical indicating whether to show the node
34 labels on the phylogeny (defaults to \code{FALSE}, i.e. the labels
36 \item{edge.color}{a vector of mode character giving the colours used
37 to draw the branches of the plotted phylogeny. These are taken to be
38 in the same order than the component \code{edge} of \code{phy}. If
39 fewer colours are given than the length of \code{edge}, then the
40 colours are recycled.}
41 \item{edge.width}{a numeric vector giving the width of the branches of
42 the plotted phylogeny. These are taken to be in the same order than
43 the component \code{edge} of \code{phy}. If fewer widths are given
44 than the length of \code{edge}, then these are recycled.}
45 \item{edge.lty}{same than the previous argument but for line types;
46 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash.}
47 \item{font}{an integer specifying the type of font for the labels: 1
48 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold
50 \item{cex}{a numeric value giving the factor scaling of the tip and
51 node labels (Character EXpansion). The default is to take the
52 current value from the graphical parameters.}
53 \item{adj}{a numeric specifying the justification of the text strings
54 of the labels: 0 (left-justification), 0.5 (centering), or 1
55 (right-justification). This option has no effect if \code{type =
56 "unrooted"}. If \code{NULL} (the default) the value is set with
57 respect of \code{direction} (see details).}
58 \item{srt}{a numeric giving how much the labels are rotated in degrees
59 (negative values are allowed resulting in clock-like rotation); the
60 value has an effect respectively to the value of
61 \code{direction} (see Examples). This option has no effect if
62 \code{type = "unrooted"}.}
63 \item{no.margin}{a logical. If \code{TRUE}, the margins are set to
64 zero and the plot uses all the space of the device (note that this
65 was the behaviour of \code{plot.phylo} up to version 0.2-1 of `ape'
66 with no way to modify it by the user, at least easily).}
67 \item{root.edge}{a logical indicating whether to draw the root edge
68 (defaults to FALSE); this has no effect if `use.edge.length = FALSE'
69 or if `type = "unrooted"'.}
70 \item{label.offset}{a numeric giving the space between the nodes and
71 the tips of the phylogeny and their corresponding labels. This
72 option has no effect if \code{type = "unrooted"}.}
73 \item{underscore}{a logical specifying whether the underscores in tip
74 labels should be written as spaces (the default) or left as are (if
76 \item{x.lim}{a numeric vector of length one or two giving the limit(s)
77 of the x-axis. If \code{NULL}, this is computed with respect to
78 various parameters such as the string lengths of the labels and the
79 branch lengths. If a single value is given, this is taken as the
81 \item{y.lim}{same than above for the y-axis.}
82 \item{direction}{a character string specifying the direction of the
83 tree. Four values are possible: "rightwards" (the default),
84 "leftwards", "upwards", and "downwards".}
85 \item{lab4ut}{(= labels for unrooted trees) a character string
86 specifying the display of tip labels for unrooted trees: either
87 \code{"horizontal"} where all labels are horizontal (the default),
88 or \code{"axial"} where the labels are displayed in the axis of the
89 corresponding terminal branches. This option has an effect only if
90 \code{type = "unrooted"}.}
91 \item{tip.color}{the colours used for the tip labels, eventually
92 recycled (see examples).}
93 \item{layout}{the number of trees to be plotted simultaneously.}
94 \item{\dots}{further arguments to be passed to \code{plot} or to
98 These functions plot phylogenetic trees on the current graphical
102 If \code{x} is a list of trees (i.e., an object of class
103 \code{"multiPhylo"}), then any further argument may be passed with
104 \code{...} and could be any one of those listed above for a single
107 The font format of the labels of the nodes and the tips is the same.
109 If \code{no.margin = TRUE}, the margins are set to zero and are not
110 restored after plotting the tree, so that the user can access the
111 coordinates system of the plot.
113 The option `node.pos' allows the user to alter the vertical position
114 (i.e. ordinates) of the nodes. If \code{node.pos = 1}, then the
115 ordinate of a node is the mean of the ordinates of its direct
116 descendants (nodes and/or tips). If \code{node.pos = 2}, then the
117 ordinate of a node is the mean of the ordinates of all the tips of
118 which it is the ancestor. If \code{node.pos = NULL} (the default),
119 then its value is determined with respect to other options: if
120 \code{type = "phylogram"} then `node.pos = 1'; if \code{type =
121 "cladogram"} and \code{use.edge.length = FALSE} then `node.pos = 2';
122 if \code{type = "cladogram"} and \code{use.edge.length = TRUE} then
123 `node.pos = 1'. Remember that in this last situation, the branch
124 lengths make sense when projected on the x-axis.
126 If \code{adj} is not specified, then the value is determined with
127 respect to \code{direction}: if \code{direction = "leftwards"} then
128 \code{adj = 1} (0 otherwise).
130 If the arguments \code{x.lim} and \code{y.lim} are not specified by the
131 user, they are determined roughly by the function. This may not always
132 give a nice result: the user may check these values with the
133 (invisibly) returned list (see ``Value:'').
135 If you resize manually the graphical device (windows or X11) you may
136 need to replot the tree.
139 The argument \code{asp} cannot be passed with \code{\dots}.
142 \code{plot.phylo} returns invisibly a list with the following
143 components which values are those used for the current plot:
146 \item{use.edge.length}{}
148 \item{show.tip.label}{}
149 \item{show.node.label}{}
155 \item{label.offset}{}
163 \author{Emmanuel Paradis}
165 \code{\link{read.tree}}, \code{\link{trex}}, \code{\link{kronoviz}},
166 \code{\link{add.scale.bar}}, \code{\link{axisPhylo}},
167 \code{\link{nodelabels}}, \code{\link{edges}},
168 \code{\link[graphics]{plot}} for the basic plotting function in R
171 ### An extract from Sibley and Ahlquist (1990)
172 cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
173 "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
174 file = "ex.tre", sep = "\n")
175 tree.owls <- read.tree("ex.tre")
177 unlink("ex.tre") # delete the file "ex.tre"
179 ### Show the types of trees.
180 layout(matrix(1:6, 3, 2))
181 plot(tree.owls, main = "With branch lengths")
182 plot(tree.owls, type = "c")
183 plot(tree.owls, type = "u")
184 plot(tree.owls, use.edge.length = FALSE, main = "Without branch lengths")
185 plot(tree.owls, type = "c", use.edge.length = FALSE)
186 plot(tree.owls, type = "u", use.edge.length = FALSE)
190 ### using random colours and thickness
192 edge.color = sample(colors(), length(bird.orders$edge)/2),
193 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
194 title("Random colours and branch thickness")
195 ### rainbow colouring...
196 X <- c("red", "orange", "yellow", "green", "blue", "purple")
198 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
199 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
200 title("Rainbow colouring")
201 plot(bird.orders, type = "c", use.edge.length = FALSE,
202 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
203 edge.width = rep(5, length(bird.orders$edge)/2))
204 segments(rep(0, 6), 6.5:1.5, rep(2, 6), 6.5:1.5, lwd = 5, col = X)
205 text(rep(2.5, 6), 6.5:1.5, paste(X, "..."), adj = 0)
206 title("Character mapping...")
207 plot(bird.orders, "u", font = 1, cex = 0.75)
209 plot(bird.families, "u", lab4ut = "axial", font = 1, cex = 0.5)
210 plot(bird.families, "r", font = 1, cex = 0.5)
211 ### cladogram with oblique tip labels
212 plot(bird.orders, "c", FALSE, direction = "u", srt = -40, x.lim = 25.5)
213 ### facing trees with different informations...
215 tr$tip.label <- rep("", 23)
216 layout(matrix(1:2, 1, 2), c(5, 4))
217 plot(bird.orders, "c", FALSE, adj = 0.5, no.margin = TRUE, label.offset = 0.8,
218 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
219 edge.width = rep(5, length(bird.orders$edge)/2))
220 text(7.5, 23, "Facing trees with\ndifferent informations", font = 2)
221 plot(tr, "p", direction = "l", no.margin = TRUE,
222 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
223 ### Recycling of arguments gives a lot of possibilities
225 plot(bird.orders, tip.col = c(rep("red", 5), rep("blue", 18)),
226 font = c(rep(3, 5), rep(2, 17), 1))
227 plot(bird.orders, tip.col = c("blue", "green"),
228 cex = 23:1/23 + .3, font = 1:3)
229 co <- c(rep("blue", 9), rep("green", 35))
230 plot(bird.orders, "f", edge.col = co)
231 plot(bird.orders, edge.col = co)