traitData.plot: plot a univariate continuous trait data on a phylogeny

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

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)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.