add.color.bar

This function adds a color bar to a plot created by <code>plotBranchbyTrait</code>. A color bar can be added by clicking on a location within the plot (when <code>prompt=TRUE</code>) or by setting <code>prompt=FALSE</code> and supplying x &amp; y coordinates for the object. This function is also used internally by S3 methods <code>plot.contMap</code> and <code>plot.densityMap</code>, as well as by <code>errorbar.contMap</code>.

utilities

phylogenetics

comparative method

plotting

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.color.bar function

<dl>	<dt>leg</dt>
<dd>numerical value for the length of the legend.</dd>	<dt>cols</dt>
<dd>colors for the legend.</dd>	<dt>title</dt>
<dd>text to plot above the bar.</dd>	<dt>lims</dt>
<dd>range for the bar.</dd>	<dt>digits</dt>
<dd>digits for plotted numbers.</dd>	<dt>prompt</dt>
<dd>logical value indicating whether the location of the legend should be obtained interactively.</dd>	<dt>lwd</dt>
<dd>width of the plotted bar.</dd>	<dt>outline</dt>
<dd>logical value indicated whether or not to outline the plotted color bar with a 1 pt line.</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; <code>subtitle</code> optional legend subtitle; <code>direction</code> direction of the color bar (i.e., increase from left to right or from right to left); and <code>fsize</code>, font size for the legend text.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.2-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Add color bar to a plot — add.color.bar

<dl>

	<dt>leg</dt>
<dd>numerical value for the length of the legend.</dd>

	<dt>cols</dt>
<dd>colors for the legend.</dd>

	<dt>title</dt>
<dd>text to plot above the bar.</dd>

	<dt>lims</dt>
<dd>range for the bar.</dd>

	<dt>digits</dt>
<dd>digits for plotted numbers.</dd>

	<dt>prompt</dt>
<dd>logical value indicating whether the location of the legend should be obtained interactively.</dd>

	<dt>lwd</dt>
<dd>width of the plotted bar.</dd>

	<dt>outline</dt>
<dd>logical value indicated whether or not to outline the plotted color bar with a 1 pt line.</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; <code>subtitle</code> optional legend subtitle; <code>direction</code> direction of the color bar (i.e., increase from left to right or from right to left); and <code>fsize</code>, font size for the legend text.</dd>

</dl>

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

add.color.bar: Add color bar to a plot

Description

Usage

Arguments

Author

References

See Also