colorTrees

<code>colorTree</code> Gets a color palette for a predefined set of trait values

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

colorTrees function

<dl><dt>trees</dt>
<dd>list of phylo objects with assigned internal node states</dd>
<dt>palette</dt>
<dd>named vector of colors (see getPalette)</dd>
<dt>ambig</dt>
<dd>how should ambiguous states be colored (blend or grey)</dd></dl>

Arguments

Get a color palette for a predefined set of trait values — colorTrees

<dl>

<dt>trees</dt>
<dd>list of phylo objects with assigned internal node states</dd>


<dt>palette</dt>
<dd>named vector of colors (see getPalette)</dd>


<dt>ambig</dt>
<dd>how should ambiguous states be colored (blend or grey)</dd>

</dl>

colorTrees: Get a color palette for a predefined set of trait values

Description

Usage

Value

Arguments

Details

See Also