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, 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{font}{an integer specifying the type of font for the labels: 1
46 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold
48 \item{cex}{a numeric value giving the factor scaling of the tip and
49 node labels (Character EXpansion). The default is to take the
50 current value from the graphical parameters.}
51 \item{adj}{a numeric specifying the justification of the text strings
52 of the labels: 0 (left-justification), 0.5 (centering), or 1
53 (right-justification). This option has no effect if \code{type =
54 "unrooted"}. If \code{NULL} (the default) the value is set with
55 respect of \code{direction} (see details).}
56 \item{srt}{a numeric giving how much the labels are rotated in degrees
57 (negative values are allowed resulting in clock-like rotation); the
58 value has an effect respectively to the value of
59 \code{direction} (see Examples). This option has no effect if
60 \code{type = "unrooted"}.}
61 \item{no.margin}{a logical. If \code{TRUE}, the margins are set to
62 zero and the plot uses all the space of the device (note that this
63 was the behaviour of \code{plot.phylo} up to version 0.2-1 of `ape'
64 with no way to modify it by the user, at least easily).}
65 \item{root.edge}{a logical indicating whether to draw the root edge
66 (defaults to FALSE); this has no effect if `use.edge.length = FALSE'
67 or if `type = "unrooted"'.}
68 \item{label.offset}{a numeric giving the space between the nodes and
69 the tips of the phylogeny and their corresponding labels. This
70 option has no effect if \code{type = "unrooted"}.}
71 \item{underscore}{a logical specifying whether the underscores in tip
72 labels should be written as spaces (the default) or left as are (if
74 \item{x.lim}{a numeric vector of length one or two giving the limit(s)
75 of the x-axis. If \code{NULL}, this is computed with respect to
76 various parameters such as the string lengths of the labels and the
77 branch lengths. If a single value is given, this is taken as the
79 \item{y.lim}{same than above for the y-axis.}
80 \item{direction}{a character string specifying the direction of the
81 tree. Four values are possible: "rightwards" (the default),
82 "leftwards", "upwards", and "downwards".}
83 \item{lab4ut}{(= labels for unrooted trees) a character string
84 specifying the display of tip labels for unrooted trees: either
85 \code{"horizontal"} where all labels are horizontal (the default),
86 or \code{"axial"} where the labels are displayed in the axis of the
87 corresponding terminal branches. This option has an effect only if
88 \code{type = "unrooted"}.}
89 \item{tip.color}{the colours used for the tip labels, eventually
90 recycled (see examples).}
91 \item{layout}{the number of trees to be plotted simultaneously.}
92 \item{...}{further arguments to be passed to \code{plot} or to
96 These functions plot phylogenetic trees on the current graphical
100 If \code{x} is a list of trees (i.e., an object of class
101 \code{"multiPhylo"}), then any further argument may be passed with
102 \code{...} and could be any one of those listed above for a single
105 The formatting of the labels of both the nodes and the tips is the
108 If \code{no.margin = TRUE}, the margins are set to zero and are not
109 restored after plotting the tree, so that the user can access the
110 coordinates system of the plot.
112 The option `node.pos' allows the user to alter the vertical position
113 (i.e. ordinates) of the nodes. If \code{node.pos = 1}, then the
114 ordinate of a node is the mean of the ordinates of its direct
115 descendants (nodes and/or tips). If \code{node.pos = 2}, then the
116 ordinate of a node is the mean of the ordinates of all the tips of
117 which it is the ancestor. If \code{node.pos = NULL} (the default),
118 then its value is determined with respect to other options: if
119 \code{type = "phylogram"} then `node.pos = 1'; if \code{type =
120 "cladogram"} and \code{use.edge.length = FALSE} then `node.pos = 2';
121 if \code{type = "cladogram"} and \code{use.edge.length = TRUE} then
122 `node.pos = 1'. Remember that in this last situation, the branch
123 lengths make sense when projected on the x-axis.
125 If \code{adj} is not specified, then the value is determined with
126 respect to \code{direction}: if \code{direction = "leftwards"} then
127 \code{adj = 1} (0 otherwise).
129 If the arguments \code{x.lim} and \code{y.lim} are not specified by the
130 user, they are determined roughly by the function. This may not always
131 give a nice result: the user may check these values with the
132 (invisibly) returned list (see ``Value:'').
134 Note that if you resize manually the graphical device (windows or X11)
135 you may need to replot the tree.
138 \code{plot.phylo} returns invisibly a list with the following
139 components which values are those used for the current plot:
142 \item{use.edge.length}
144 \item{show.tip.label}
145 \item{show.node.label}
159 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
161 \code{\link{read.tree}}, \code{\link{add.scale.bar}},
162 \code{\link{axisPhylo}}, \code{\link{nodelabels}},
163 \code{\link[graphics]{plot}} for the basic
164 plotting function in R
167 ### An extract from Sibley and Ahlquist (1990)
168 cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
169 "Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
170 file = "ex.tre", sep = "\n")
171 tree.owls <- read.tree("ex.tre")
173 unlink("ex.tre") # delete the file "ex.tre"
175 ### Show the types of trees.
176 layout(matrix(1:6, 3, 2))
177 plot(tree.owls, main = "With branch lengths")
178 plot(tree.owls, type = "c")
179 plot(tree.owls, type = "u")
180 plot(tree.owls, use.edge.length = FALSE, main = "Without branch lengths")
181 plot(tree.owls, type = "c", use.edge.length = FALSE)
182 plot(tree.owls, type = "u", use.edge.length = FALSE)
187 ### remove the margins...
188 plot(xenarthra, no.margin = TRUE)
189 ### ... and use a smaller font size
190 plot(xenarthra, no.margin = TRUE, cex = 0.8)
191 plot(xenarthra, type = "c", no.margin = TRUE,
192 use.edge.length = FALSE, cex = 0.8)
193 par(mar = c(5.1, 4.1, 4.1, 2.1))
196 ### using random colours and thickness
198 edge.color = sample(colors(), length(bird.orders$edge)/2),
199 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
200 title("Random colours and branch thickness")
201 ### rainbow colouring...
202 X <- c("red", "orange", "yellow", "green", "blue", "purple")
204 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
205 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
206 title("Rainbow colouring")
207 plot(bird.orders, type = "c", use.edge.length = FALSE,
208 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
209 edge.width = rep(5, length(bird.orders$edge)/2))
210 segments(rep(0, 6), 6.5:1.5, rep(2, 6), 6.5:1.5, lwd = 5, col = X)
211 text(rep(2.5, 6), 6.5:1.5, paste(X, "..."), adj = 0)
212 title("Character mapping...")
213 plot(bird.orders, "u", font = 1, cex = 0.75)
215 plot(bird.families, "u", lab4ut = "axial", font = 1, cex = 0.5)
216 plot(bird.families, "r", font = 1, cex = 0.5)
217 ### cladogram with oblique tip labels
218 plot(bird.orders, "c", FALSE, direction = "u", srt = -40, x.lim = 25.5)
219 ### facing trees with different informations...
221 tr$tip.label <- rep("", 23)
222 layout(matrix(1:2, 1, 2), c(5, 4))
223 plot(bird.orders, "c", FALSE, adj = 0.5, no.margin = TRUE, label.offset = 0.8,
224 edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
225 edge.width = rep(5, length(bird.orders$edge)/2))
226 text(7.5, 23, "Facing trees with\ndifferent informations", font = 2)
227 plot(tr, "p", direction = "l", no.margin = TRUE,
228 edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
229 ### Recycling of arguments gives a lot of possibilities
231 plot(bird.orders, tip.col = c(rep("red", 5), rep("blue", 18)),
232 font = c(rep(3, 5), rep(2, 17), 1))
233 plot(bird.orders, tip.col = c("blue", "green"),
234 cex = 23:1/23 + .3, font = 1:3)
235 co <- c(rep("blue", 9), rep("green", 35))
236 plot(bird.orders, "f", edge.col = co)
237 plot(bird.orders, edge.col = co)