add.simmap.legend

states for the discrete character in the order of <code>colors</code>.

colors for the legend in the order of <code>leg</code>, or, if <code>leg=NULL</code>, named vector of colors in which <code>names(colors</code> are the states of the mapped discrete character.

colors

logical value indicating whether the location of the legend should be obtained interactively (i.e., by clicking in the plotting area).

prompt

logical value indiciating whether to plot the legend vertically (if <code>TRUE</code>) or horizontally.

vertical

optional arguments including: <code>x</code> x-coordinate of the legend (if <code>prompt=FALSE</code>); <code>y</code> y-coordinate of the legend; and <code>shape</code> which can be <code>shape="square"</code>, the default, or <code>shape="circle"</code>.

This function adds a legend (by default, interactively) to a plotted stochastic character mapped tree.

utilities

phylogenetics

comparative method

plotting

discrete character

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

add.simmap.legend function

<dl>	<dt>leg</dt>
<dd>states for the discrete character in the order of <code>colors</code>.</dd>	<dt>colors</dt>
<dd>colors for the legend in the order of <code>leg</code>, or, if <code>leg=NULL</code>, named vector of colors in which <code>names(colors</code> are the states of the mapped discrete character.</dd>	<dt>prompt</dt>
<dd>logical value indicating whether the location of the legend should be obtained interactively (i.e., by clicking in the plotting area).</dd>	<dt>vertical</dt>
<dd>logical value indiciating whether to plot the legend vertically (if <code>TRUE</code>) or horizontally.</dd>	<dt>...</dt>
<dd>optional arguments including: <code>x</code> x-coordinate of the legend (if <code>prompt=FALSE</code>); <code>y</code> y-coordinate of the legend; and <code>shape</code> which can be <code>shape="square"</code>, the default, or <code>shape="circle"</code>.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.0-3" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Add legend to stochastically mapped tree — add.simmap.legend

<dl>

	<dt>leg</dt>
<dd>states for the discrete character in the order of <code>colors</code>.</dd>

	<dt>colors</dt>
<dd>colors for the legend in the order of <code>leg</code>, or, if <code>leg=NULL</code>, named vector of colors in which <code>names(colors</code> are the states of the mapped discrete character.</dd>

	<dt>prompt</dt>
<dd>logical value indicating whether the location of the legend should be obtained interactively (i.e., by clicking in the plotting area).</dd>

	<dt>vertical</dt>
<dd>logical value indiciating whether to plot the legend vertically (if <code>TRUE</code>) or horizontally.</dd>

	<dt>...</dt>
<dd>optional arguments including: <code>x</code> x-coordinate of the legend (if <code>prompt=FALSE</code>); <code>y</code> y-coordinate of the legend; and <code>shape</code> which can be <code>shape="square"</code>, the default, or <code>shape="circle"</code>.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

add.simmap.legend: Add legend to stochastically mapped tree

Description

Usage

Arguments

Author

References

See Also