splitplotTree

plotTree.splits

Function plots a tree in two columns or windows.

phylogenetics

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)

splitplotTree function

<dl> 	<dt>tree</dt>
<dd>an object of class "phylo".</dd> 	<dt>fsize</dt>
<dd>relative font size for tip labels.</dd>	<dt>ftype</dt>
<dd>font type - options are <code>"reg"</code>, <code>"i"</code> (italics), <code>"b"</code> (bold), or <code>"bi"</code> (bold-italics).</dd>	<dt>lwd</dt>
<dd>line width for plotting.</dd>	<dt>split</dt>
<dd>relative vertical position for splitting the tree (between 0 &amp; 1).</dd>	<dt>new.window</dt>
<dd>whether or not to plot the split tree in a new window. If <code>FALSE</code> then the tree will be plotted in two columns within the same plotting window.</dd>	<dt>splits</dt>
<dd>for <code>plotTree.splits</code> relative positions (from 0 to 1) to split the tree across pages or devices.</dd>	<dt>file</dt>
<dd>filename if saving to a PDF file is desired. Otherwise will plot to the default plotting device.</dd>	<dt>fn</dt>
<dd>function to be executed on each plotted page. For instance, might be: <code>function()</code> <code>cladelabels()</code> if clade labels are desired.</dd>	<dt>...</dt>
<dd>other arguments to be passed to <code>plotTree</code>.</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

Plots a phylogeny in two columns — splitplotTree

<dl>

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

 	<dt>fsize</dt>
<dd>relative font size for tip labels.</dd>

	<dt>ftype</dt>
<dd>font type - options are <code>"reg"</code>, <code>"i"</code> (italics), <code>"b"</code> (bold), or <code>"bi"</code> (bold-italics).</dd>

	<dt>lwd</dt>
<dd>line width for plotting.</dd>

	<dt>split</dt>
<dd>relative vertical position for splitting the tree (between 0 &amp; 1).</dd>

	<dt>new.window</dt>
<dd>whether or not to plot the split tree in a new window. If <code>FALSE</code> then the tree will be plotted in two columns within the same plotting window.</dd>

	<dt>splits</dt>
<dd>for <code>plotTree.splits</code> relative positions (from 0 to 1) to split the tree across pages or devices.</dd>

	<dt>file</dt>
<dd>filename if saving to a PDF file is desired. Otherwise will plot to the default plotting device.</dd>

	<dt>fn</dt>
<dd>function to be executed on each plotted page. For instance, might be: <code>function()</code> <code>cladelabels()</code> if clade labels are desired.</dd>

	<dt>...</dt>
<dd>other arguments to be passed to <code>plotTree</code>.</dd>

</dl>

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

splitplotTree: Plots a phylogeny in two columns

Description

Usage

Value

Arguments

Author

References

See Also