scaleBranches

<code>scaleBranches</code> Branch length scaling function.

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

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

scaleBranches function

<dl><dt>clones</dt>
<dd>a tibble of <code>airrClone</code> and <code>phylo</code> objects,
the output of getTrees.</dd>
<dt>edge_type</dt>
<dd>Either <code>genetic_distance</code> (mutations per site) or 
<code>mutations</code></dd></dl>

Arguments

Scale branch lengths to represent either mutations or mutations per site. — scaleBranches

<dl>

<dt>clones</dt>
<dd>a tibble of <code>airrClone</code> and <code>phylo</code> objects,
the output of getTrees.</dd>


<dt>edge_type</dt>
<dd>Either <code>genetic_distance</code> (mutations per site) or 
<code>mutations</code></dd>

</dl>

scaleBranches: Scale branch lengths to represent either mutations or mutations per site.

Description

Usage

Value

Arguments

Details

See Also