add.simmap.legend

Adds a legend (by default, interactively) to a plotted stochastic character mapped tree.

utilities

phylogenetics

comparative method

plotting

discrete character

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, 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 trait data. 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 phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range 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 indicating 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=2.1-1" 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 indicating 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

Details

References

See Also