Plot Phylogenies
These functions plot phylogenetic trees on the current graphical device.
## S3 method for class 'phylo'
plot(x, type = "phylogram", use.edge.length = TRUE,
node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE,
edge.color = "black", edge.width = 1, edge.lty = 1, font = 3,
cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
lab4ut = NULL, tip.color = "black", plot = TRUE,
rotate.tree = 0, open.angle = 0, node.depth = 1,
align.tip.label = FALSE, ...)
## S3 method for class 'multiPhylo'
plot(x, layout = 1, ...)x |
an object of class |
type |
a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial" or any unambiguous abbreviation of these. |
use.edge.length |
a logical indicating whether to use the edge
lengths of the phylogeny to draw the branches (the default) or not
(if |
node.pos |
a numeric taking the value 1 or 2 which specifies the
vertical position of the nodes with respect to their descendants. If
|
show.tip.label |
a logical indicating whether to show the tip
labels on the phylogeny (defaults to |
show.node.label |
a logical indicating whether to show the node
labels on the phylogeny (defaults to |
edge.color |
a vector of mode character giving the colours used
to draw the branches of the plotted phylogeny. These are taken to be
in the same order than the component |
edge.width |
a numeric vector giving the width of the branches of
the plotted phylogeny. These are taken to be in the same order than
the component |
edge.lty |
same than the previous argument but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash. |
font |
an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic). |
cex |
a numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters. |
adj |
a numeric specifying the justification of the text strings
of the labels: 0 (left-justification), 0.5 (centering), or 1
(right-justification). This option has no effect if |
srt |
a numeric giving how much the labels are rotated in degrees
(negative values are allowed resulting in clock-like rotation); the
value has an effect respectively to the value of
|
no.margin |
a logical. If |
root.edge |
a logical indicating whether to draw the root edge (defaults to FALSE); this has no effect if ‘use.edge.length = FALSE’ or if ‘type = "unrooted"’. |
label.offset |
a numeric giving the space between the nodes and
the tips of the phylogeny and their corresponding labels. This
option has no effect if |
underscore |
a logical specifying whether the underscores in tip
labels should be written as spaces (the default) or left as are (if
|
x.lim |
a numeric vector of length one or two giving the limit(s)
of the x-axis. If |
y.lim |
same than above for the y-axis. |
direction |
a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards". |
lab4ut |
(= labels for unrooted trees) a character string
specifying the display of tip labels for unrooted trees (can be
abbreviated): either |
tip.color |
the colours used for the tip labels, eventually recycled (see examples). |
plot |
a logical controlling whether to draw the tree. If
|
rotate.tree |
for "fan", "unrooted", or "radial" trees: the rotation of the whole tree in degrees (negative values are accepted). |
open.angle |
if |
node.depth |
an integer value (1 or 2) used if branch lengths are not used to plot the tree; 1: the node depths are proportional to the number of tips descending from each node (the default and was the only possibility previously), 2: they are evenly spaced. |
align.tip.label |
a logical value or an integer. If |
layout |
the number of trees to be plotted simultaneously. |
... |
further arguments to be passed to |
If x is a list of trees (i.e., an object of class
"multiPhylo"), then any further argument may be passed with
... and could be any one of those listed above for a single
tree.
The font format of the labels of the nodes and the tips is the same.
If no.margin = TRUE, the margins are set to zero and are not
restored after plotting the tree, so that the user can access the
coordinates system of the plot.
The option ‘node.pos’ allows the user to alter the vertical position
(i.e., ordinates) of the nodes. If node.pos = 1, then the
ordinate of a node is the mean of the ordinates of its direct
descendants (nodes and/or tips). If node.pos = 2, then the
ordinate of a node is the mean of the ordinates of all the tips of
which it is the ancestor. If node.pos = NULL (the default),
then its value is determined with respect to other options: if
type = "phylogram" then ‘node.pos = 1’; if type =
"cladogram" and use.edge.length = FALSE then ‘node.pos = 2’;
if type = "cladogram" and use.edge.length = TRUE then
‘node.pos = 1’. Remember that in this last situation, the branch
lengths make sense when projected on the x-axis.
If adj is not specified, then the value is determined with
respect to direction: if direction = "leftwards" then
adj = 1 (0 otherwise).
If the arguments x.lim and y.lim are not specified by the
user, they are determined roughly by the function. This may not always
give a nice result: the user may check these values with the
(invisibly) returned list (see “Value:”).
If you use align.tip.label = TRUE with type = "fan", you
will have certainly to set x.lim and y.lim manually.
If you resize manually the graphical device (windows or X11) you may need to replot the tree.
plot.phylo returns invisibly a list with the following
components which values are those used for the current plot:
type |
|
use.edge.length |
|
node.pos |
|
node.depth |
|
show.tip.label |
|
show.node.label |
|
font |
|
cex |
|
adj |
|
srt |
|
no.margin |
|
label.offset |
|
x.lim |
|
y.lim |
|
direction |
|
tip.color |
|
Ntip |
|
Nnode |
|
root.time |
|
align.tip.label |
The argument asp cannot be passed with ....
Emmanuel Paradis
read.tree, trex, kronoviz,
add.scale.bar, axisPhylo,
nodelabels, edges,
plot for the basic plotting function in R
### An extract from Sibley and Ahlquist (1990)
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
"Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
file = "ex.tre", sep = "\n")
tree.owls <- read.tree("ex.tre")
plot(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"
### Show the types of trees.
layout(matrix(1:6, 3, 2))
plot(tree.owls, main = "With branch lengths")
plot(tree.owls, type = "c")
plot(tree.owls, type = "u")
plot(tree.owls, use.edge.length = FALSE, main = "Without branch lengths")
plot(tree.owls, type = "c", use.edge.length = FALSE)
plot(tree.owls, type = "u", use.edge.length = FALSE)
layout(1)
data(bird.orders)
### using random colours and thickness
plot(bird.orders,
edge.color = sample(colors(), length(bird.orders$edge)/2),
edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Random colours and branch thickness")
### rainbow colouring...
X <- c("red", "orange", "yellow", "green", "blue", "purple")
plot(bird.orders,
edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Rainbow colouring")
plot(bird.orders, type = "c", use.edge.length = FALSE,
edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
edge.width = rep(5, length(bird.orders$edge)/2))
segments(rep(0, 6), 6.5:1.5, rep(2, 6), 6.5:1.5, lwd = 5, col = X)
text(rep(2.5, 6), 6.5:1.5, paste(X, "..."), adj = 0)
title("Character mapping...")
plot(bird.orders, "u", font = 1, cex = 0.75)
data(bird.families)
plot(bird.families, "u", lab4ut = "axial", font = 1, cex = 0.5)
plot(bird.families, "r", font = 1, cex = 0.5)
### cladogram with oblique tip labels
plot(bird.orders, "c", FALSE, direction = "u", srt = -40, x.lim = 25.5)
### facing trees with different informations...
tr <- bird.orders
tr$tip.label <- rep("", 23)
layout(matrix(1:2, 1, 2), c(5, 4))
plot(bird.orders, "c", FALSE, adj = 0.5, no.margin = TRUE, label.offset = 0.8,
edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
edge.width = rep(5, length(bird.orders$edge)/2))
text(7.5, 23, "Facing trees with\ndifferent informations", font = 2)
plot(tr, "p", direction = "l", no.margin = TRUE,
edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
### Recycling of arguments gives a lot of possibilities
### for tip labels:
plot(bird.orders, tip.col = c(rep("red", 5), rep("blue", 18)),
font = c(rep(3, 5), rep(2, 17), 1))
plot(bird.orders, tip.col = c("blue", "green"),
cex = 23:1/23 + .3, font = 1:3)
co <- c(rep("blue", 9), rep("green", 35))
plot(bird.orders, "f", edge.col = co)
plot(bird.orders, edge.col = co)
layout(1)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.