Function plots a tree with branches colored by the value for a quantitative trait or probability, by various methods.

plotBranchbyTrait

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)

plotBranchbyTrait function

Plot branch colors by a quantitative trait or value — plotBranchbyTrait

<dl>

	<dt>tree</dt>
<dd>an object of class <code>"phylo"</code>.</dd>

	<dt>x</dt>
<dd>either a vector of states for the edges, tips, or nodes of the tree (for <code>mode="edges"</code>, <code>"tips"</code>, and <code>"nodes"</code>, respectively).</dd>

	<dt>mode</dt>
<dd>string indicating plotting mode. <code>mode="edges"</code>, the default, requires that the mapping state of each edge in the tree should be provided. <code>mode="tips"</code> takes the tip values and estimates the state at each internal node. The mapped character value along each branch is the average of the nodes subtending that branch. <code>mode="nodes"</code> similar to <code>"tips"</code>, except that the node values are provided instead of estimated.</dd>

	<dt>palette</dt>
<dd>color palette to translate character values to color. Options are presently <code>"rainbow"</code> (the default), <code>"heat.colors"</code>, and <code>"gray"</code>. <code>palette</code> can also be a function produced by <code><a href='https://rdrr.io/r/grDevices/colorRamp.html'>colorRampPalette</a></code>.</dd>

	<dt>legend</dt>
<dd>can be a logical value (<code>TRUE</code> or <code>FALSE</code>) or a numeric value greater than 0. In the latter case the numeric value gives the length of the plotted legend, which also acts as a scale bar for the branch lengths of the tree.</dd>

	<dt>xlims</dt>
<dd>range for the translation map between trait values and the color map. Should be inclusive of all the values in <code>x</code>.</dd>

	<dt>...</dt>
<dd>other optional arguments to be passed to <code>plot.phylo</code> - pretty much all arguments are available. In addition, there <code>plotBranchbyTrait</code> has the following additional optional arguments: <code>tol</code> a small tolerance value to be added to the range of <code>x</code>; <code>prompt</code> for <code>legend=TRUE</code>, a logical value indicating whether to prompt for the position of the legend (or not) - the default is to put the legend in the lower left hand size of the plot; <code>title</code> for <code>legend=TRUE</code>, the title of the legend; and <code>digits</code> for <code>legend=TRUE</code>, the number of digits in the quantitative scale of the legend. Finally, <code>cex</code> can be supplied as either a single numeric value, or as a vector of two different values. If the latter is true than the second element of <code>cex</code> will be passed internally to the function <code>add.color.bar</code>.</dd>

</dl>

Arguments

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

plotBranchbyTrait: Plot branch colors by a quantitative trait or value

Description

Usage

Arguments

Value

Details

References