quartetBTinferencePlot

Plot a 2-d probability simplex, with points for all normalized quartet count
vectors. Colors indicate B- or T-quartets from TINNIK algorithm, at specified
test levels.

Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forthcoming).
Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

John Rhodes

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Elizabeth Allman

Hector Banos

Jonathan Mitchell

Kristina Wicke

quartetBTinferencePlot function

<dl><dt>pTable</dt>
<dd>table of quartets and p-values</dd>
<dt>Bquartets</dt>
<dd>indicator vector for B-quartets (1=B, 0=T), ordered as in pTable</dd>
<dt>test</dt>
<dd>test model used for tree null hypothesis; options are <code>"cut"</code>, <code>"T3"</code></dd>
<dt>alpha</dt>
<dd>significance level used by TINNIK for test <code>test</code></dd>
<dt>beta</dt>
<dd>significance level used by TINNIK for star tree test</dd>
<dt>cex</dt>
<dd>scaling factor for size of plotted symbols</dd></dl>

Arguments

Produce simplex plot with  results of B/T-quartet inference — quartetBTinferencePlot

<dl>

<dt>pTable</dt>
<dd>table of quartets and p-values</dd>


<dt>Bquartets</dt>
<dd>indicator vector for B-quartets (1=B, 0=T), ordered as in pTable</dd>


<dt>test</dt>
<dd>test model used for tree null hypothesis; options are <code>"cut"</code>, <code>"T3"</code></dd>


<dt>alpha</dt>
<dd>significance level used by TINNIK for test <code>test</code></dd>


<dt>beta</dt>
<dd>significance level used by TINNIK for star tree test</dd>


<dt>cex</dt>
<dd>scaling factor for size of plotted symbols</dd>

</dl>

quartetBTinferencePlot: Produce simplex plot with results of B/T-quartet inference

Description

Usage

Arguments

Details

See Also

Examples