plotSkylines

<code>plotSkylines</code> Simple Bayesian skyline plots

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

plotSkylines function

<dl><dt>clones</dt>
<dd>output from getTrees using BEAST</dd>
<dt>file</dt>
<dd>pdf file name for printing plots</dd>
<dt>width</dt>
<dd>width of plot in inches if file specified</dd>
<dt>height</dt>
<dd>height of plot in inches if file specified</dd>
<dt>...</dt>
<dd>optional arguments passed to grDevices::pdf</dd></dl>

Arguments

Simple function for plotting Bayesian skyline plots — plotSkylines

<dl>

<dt>clones</dt>
<dd>output from getTrees using BEAST</dd>


<dt>file</dt>
<dd>pdf file name for printing plots</dd>


<dt>width</dt>
<dd>width of plot in inches if file specified</dd>


<dt>height</dt>
<dd>height of plot in inches if file specified</dd>


<dt>...</dt>
<dd>optional arguments passed to grDevices::pdf</dd>

</dl>

plotSkylines: Simple function for plotting Bayesian skyline plots

Description

Usage

Value

Arguments

See Also