traitData.plot {motmot}

plot a univariate continuous trait data on a phylogeny

Description

Plots a phylogeny with lines representing the value of a continuous trait

Usage

traitData.plot(
  y,
  phy,
  col.label = "red",
  col.tree = "black",
  col.hist = "navy",
  cex.plot = 0.7,
  cex.tips = 0.7,
  show.tips = FALSE,
  include.hist = FALSE,
  n.split = 5,
  lwd.traits = 1,
  show.axis = TRUE,
  axis.text = NULL,
  transform.axis.label = NULL,
  at = NULL,
  labels = NULL,
  axis.text.line = 1,
  offset.bars = 1,
  ...
)

Arguments

y

A matrix of trait values with taxon names as rownames.

phy

An object of class phylo (see ape).

col.label

colour labels for the traits at the tips and in the histogram

col.tree

colour for the edge labels on the tree

col.hist

colour of the histogram

cex.plot

Numeric. The size of labels for the histogram axis labels

cex.tips

Numeric. The size of the phylogeny tip labels

show.tips

Logical. If FALSE (default), no tip labels are shown. If TRUE, tip labels are shown

include.hist

Logical. Include a histrogram alongside the plot of the tree?

n.split

Numeric. The number of splits for the axis labels and shading for the trait values

lwd.traits

Line widths of traits shown on the plot

show.axis

Logical. If TRUE, shows the axis of trait values on the plot.

axis.text

text shown above the trait label axis. If NULL (default), nothing is displayed

transform.axis.label

If the data are provided as logarithms the labels for trait axis can be transformed to their original values by calculating the exponential function of the natural (transform.axis.label="exp") or base 10 logarithm. The default (NULL) leaves the labels un-transformed.

at

Axis tick point locations for if show.axis is TRUE.

labels

Axis labels locations for if show.axis is TRUE.

axis.text.line

The location of the label for the trait axis beside the plot.

offset.bars

The distance of trait plot lines from the phylogeny.

...

further arguments passed to the axis function

Value

A plot with the trait values shown at the tips, and a histrogram of the trait values

Author(s)

Mark Puttick

Examples

data(anolis.tree)
data(anolis.data)
attach(anolis.data)
male.length <- matrix(Male_SVL, dimnames=list(rownames(anolis.data)))
sortedData <- sortTraitData(anolis.tree, male.length)
phy <- sortedData$phy
male.length <- sortedData$trait
traitData.plot(y=male.length, phy)