plot.phyloLayout: plot.phyloLayout

In ArtPoon/ggfree: ggplot2-style plots with base R graphics

plot.phyloLayout

Description

Generic plot function for phylogenetic trees with layouts generated using ggfree. The coordinate system of the plot depends on the layout algorithm:

Rectangular/slanted layout: The x-axis is scaled to the height of the tree (from the root to the furthest tip). The y-axis is scaled to the number of tips (1:Ntip(phy)).

Circular (radial) layout: Graphical parameters such as 'col' or 'lwd' can take either a single value or a vector to specify custom values for each edge. The ordering should be the same as the original tree (phylo) object, which defaults to preorder traversal.

Usage

## S3 method for class 'phyloLayout'
plot(
  obj,
  type = "l",
  col = "grey50",
  lwd = 2,
  label = "t",
  cex.lab = 0.8,
  mar = NA,
  xlim = NA,
  add = FALSE,
  offset = 0,
  ...
)

Arguments

obj:	S3 object of class 'phyloLayout'
type:	if 'n', then line segments are not drawn
col:	colour for line segments. Defaults to 'grey50'.
lwd:	stroke width for line segments. Defaults to 2.
label:	Specifies whether nodes are labeled with text. 'n'No node labels. 't'Tip labels only (default). 'i'Internal node labels only. 'b'Both tip and internal node labels.
cex.lab:	Character expansion factor for node labels (default 0.8).
mar:	(optional) vector of margin widths (graphical parameter).
...:	additional graphical parameters to pass to 'lines' and 'label'

Examples

# generate random coalescent tree
set.seed(1999); phy <- rcoal(50)

# rectangular tree
plot(tree.layout(phy, type='r'), mar=c(3,0,0,1))
axis(side=1)

# unscaled slanted tree with colors
pal <- colorRampPalette(c('cadetblue', 'brown'))
plot(tree.layout(phy, type='s', unscaled=TRUE), col=pal(5))

# unrooted tree
plot(tree.layout(phy, type='u'))

# circular (radial) tree
plot(tree.layout(phy, type='o'), label='t')

ArtPoon/ggfree documentation built on July 11, 2024, 11:15 a.m.