ape (version 1.2-4)

plot.phylo: Plot Phylogenies

Description

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

Usage

## S3 method for class 'phylo':
plot(x, type = "phylogram", use.edge.length = TRUE,
             node.pos = NULL, show.node.label = FALSE,
             edge.color = NULL, edge.width = NULL, font = 3,
             adj = 0, srt = 0, no.margin = FALSE, root.edge = FALSE,
             label.offset = NULL, underscore = FALSE, x.lim = NULL, ...)

Arguments

x

an object of class "phylo".

type

a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "unrooted", 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 detail

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

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. If NULL, this is computed with respect to various parameters such as the string lengths of the labels.

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 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:
• type
• use.edge.length
• node.pos
• 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 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'. 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 the (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"

### 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(xenarthra)
op <- par()
par(ask = TRUE)
plot(xenarthra)
### remove the margins and put the tip labels closer
### to the tips
plot(xenarthra, no.margin = TRUE, label.offset = .005)
### use a smaller font size
par(cex = 0.8)
plot(xenarthra, no.margin = TRUE, label.offset = .005)
plot(xenarthra, type = "c", no.margin = TRUE, label.offset = .005, use.edge.length = FALSE)
par(op)

data(bird.orders)
### using random colours and thichness
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 is possible...")

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