getSkylines

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

Erick Matsen

Steven Kleinstein

getSkylines function

<dl><dt>clones</dt>
<dd>clone tibble</dd>
<dt>time</dt>
<dd>name of time column</dd>
<dt>bins</dt>
<dd>number of bins for plotting</dd>
<dt>verbose</dt>
<dd>if 1, print name of clones</dd>
<dt>forward</dt>
<dd>plot in forward or (FALSE) backward time?</dd>
<dt>nproc</dt>
<dd>processors for parallelization (by clone)</dd>
<dt>max_height</dt>
<dd>max height to use (min, median, mean, max)</dd>
<dt>exclude_germline</dt>
<dd>exclude germline from skyline plot? (For TyCHE GRTs)</dd></dl>

Arguments

Make data frames for Bayesian skyline plots — getSkylines

<dl>

<dt>clones</dt>
<dd>clone tibble</dd>


<dt>time</dt>
<dd>name of time column</dd>


<dt>bins</dt>
<dd>number of bins for plotting</dd>


<dt>verbose</dt>
<dd>if 1, print name of clones</dd>


<dt>forward</dt>
<dd>plot in forward or (FALSE) backward time?</dd>


<dt>nproc</dt>
<dd>processors for parallelization (by clone)</dd>


<dt>max_height</dt>
<dd>max height to use (min, median, mean, max)</dd>


<dt>exclude_germline</dt>
<dd>exclude germline from skyline plot? (For TyCHE GRTs)</dd>

</dl>

Make data frames for Bayesian skyline plots

getSkylines: Make data frames for Bayesian skyline plots

Description

Usage

Value

Arguments

Details