ape (version 1.0)

plot.phylo: Plot Phylogenies

Description

This function plots a phylogenetic tree on the current graphical device.

Usage

## S3 method for class 'phylo':
plot(x, show.node.label = FALSE, edge.color = NULL,
                     edge.width = NULL, font = 3, adj = 0, srt = 0,
                     no.margin = FALSE, label.offset = NULL,
                     x.lim = NULL, ...)

Arguments

x

an object of class "phylo".

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 o

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, th

font

an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).

adj

a numeric specifying the justification of the text strings of the labels: 0 (left-justification, the default), 0.5 (centering), or 1 (right-justification).

srt

a numeric giving how much the labels are rotated in degrees (negative values are allowed resulting in clock-like rotation).

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 le

label.offset

a numeric giving the space between the nodes and the tips of the phylogeny and their corresponding labels. If NULL, this is computed with respect to various parameters such as the string lengths of the labels.

x.lim

a numeric giving the limit 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.

...

further arguments to be passed to plot().

Value

• The function returns invisibly a list with the following components which values are those used for the current plot:
• show.node.label
• edge.color
• edge.width
• font
• adj
• srt
• no.margin
• label.offset
• x.lim

Details

The formatting of the labels of both the nodes and the tips is the same. The new default behaviour is to use the current margins rather than to set them to zero. 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 coordinate system of the plot. If the arguments label.offset and x.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 (invisibly) returned list (see ``Value:'').

See Also

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

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 = "")
tree.owls <- read.tree("ex.tre")
plot(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"