# plot.phylo

From ape v2.6-3
0th

Percentile

##### Plot Phylogenies

These functions plot phylogenetic trees on the current graphical device.

Keywords
hplot
##### Usage
## 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 = "horizontal", tip.color = "black", ...)
## S3 method for class 'multiPhylo':
plot(x, layout = 1, ...)
##### Arguments
x
an object of class "phylo" or of class "multiPhylo".
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 FALSE). This option has no effect if the object of class "phylo" has no edge.length' element.
node.pos
a numeric taking the value 1 or 2 which specifies the vertical position of the nodes with respect to their descendants. If NULL (the default), then the value is determined in relation to type' and use.edge.length' (see details).
show.tip.label
a logical indicating whether to show the tip labels on the phylogeny (defaults to TRUE, i.e. the labels are shown).
show.node.label
a logical indicating whether to show the node labels on the phylogeny (defaults to FALSE, i.e. the labels are not shown).
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 of phy. If fewer colours are given than the length of <
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 of phy. If fewer widths are given than the length of edge, then
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.
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 type = "unrooted". If NULL (the default) th
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 direction (see Examples). This option has no effect i
no.margin
a logical. If TRUE, the margins are set to zero and the plot uses all the space of the device (note that this was the behaviour of plot.phylo up to version 0.2-1 of ape' with no way to modify it by the user, at least
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 type = "unrooted".
underscore
a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE).
x.lim
a numeric vector of length one or two giving the limit(s) of the x-axis. If NULL, this is computed with respect to various parameters such as the string lengths of the labels and the branch lengths. If a single value is given, thi
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: either "horizontal" where all labels are horizontal (the default), or "axial" where the labels are displayed in
tip.color
the colours used for the tip labels, eventually recycled (see examples).
layout
the number of trees to be plotted simultaneously.
...
further arguments to be passed to plot or to plot.phylo.
##### Details

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 resize manually the graphical device (windows or X11) you may need to replot the tree.

##### Value

• 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
• show.tip.label
• show.node.label
• font
• cex
• srt
• no.margin
• label.offset
• x.lim
• y.lim
• direction
• tip.color
• Ntip
• Nnode

##### Note

The argument asp cannot be passed with ....

read.tree, add.scale.bar, axisPhylo, nodelabels, edges, plot for the basic plotting function in R

##### Aliases
• plot.phylo
• plot.multiPhylo
##### Examples
### 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 = "")
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(matrix(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$edge)/2)) text(7.5, 23, "Facing trees with different informations", font = 2) plot(tr, "p", direction = "l", no.margin = TRUE, edge.width = sample(1:10, length(bird.orders$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)
Documentation reproduced from package ape, version 2.6-3, License: GPL (>= 2)

### Community examples

Looks like there are no examples yet.