PlotQuartet

Draws a tree, highlighting the members of a specified quartet in colour.

Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.

Martin R. Smith

Quartet

Comparison of Phylogenetic Trees Using Quartet and Split
Measures

Andreas Sand

Gerth Stølting Brodal

Rolf Fagerberg

Thomas Mailund

Christian N. S. Pedersen

Jens Johansen

Morten K. Holt

PlotQuartet function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>,
or a list of such trees. The first member of <code>tree</code> will be considered
the "reference" tree.</dd>
<dt>quartet</dt>
<dd>A vector of four integers, corresponding to numbered leaves on
the tree; or a character vector specifying the labels of four leaves.</dd>
<dt>overwritePar</dt>
<dd>Logical specifying whether to use existing <code>mfrow</code> and
<code>mar</code> parameters from <code><a href="/link/par?package=Quartet&version=1.2.6" data-mini-rdoc="Quartet::par">par</a>()</code> (<code>FALSE</code>),
or to plot trees side-by-side in a new graphical device (<code>TRUE</code>).</dd>
<dt>caption</dt>
<dd>Logical specifying whether to annotate each plot to specify
whether the quartet selected is in the same or a different state to the
reference tree.</dd>
<dt>...</dt>
<dd>Additional parameters to send to
<code><a href="/link/plot()?package=Quartet&version=1.2.6" data-mini-rdoc="Quartet::plot()">plot()</a></code>.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=Quartet&version=1.2.6" data-mini-rdoc="Quartet::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Plot quartet on tree topologies — PlotQuartet

<dl>

<dt>tree</dt>
<dd>A tree of class <code>phylo</code>,
or a list of such trees. The first member of <code>tree</code> will be considered
the "reference" tree.</dd>


<dt>quartet</dt>
<dd>A vector of four integers, corresponding to numbered leaves on
the tree; or a character vector specifying the labels of four leaves.</dd>


<dt>overwritePar</dt>
<dd>Logical specifying whether to use existing <code>mfrow</code> and
<code>mar</code> parameters from <code><a href='https://rdrr.io/r/graphics/par.html'>par</a>()</code> (<code>FALSE</code>),
or to plot trees side-by-side in a new graphical device (<code>TRUE</code>).</dd>


<dt>caption</dt>
<dd>Logical specifying whether to annotate each plot to specify
whether the quartet selected is in the same or a different state to the
reference tree.</dd>


<dt>...</dt>
<dd>Additional parameters to send to
<code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot()</a></code>.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

PlotQuartet: Plot quartet on tree topologies

Description

Usage

Value

Arguments

Author

Examples