plot_linkage_df

<code>plot_linkage_df</code> plots r versus LOD, colour separated for different phases.

Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

plot_linkage_df function

<dl><dt>linkage_df</dt>
<dd>A linkage data.frame as output of <code>linkage</code>.</dd>
<dt>r_max</dt>
<dd>Maximum r value to plot</dd>
<dt>stepsize</dt>
<dd>Size of window in recombination frequency to generate mean LOD score. Larger values will reduce plot density.</dd>
<dt>add_legend</dt>
<dd>Logical, should a legend be added to the plot?</dd>
<dt>...</dt>
<dd>Arguments passed to base plot function</dd></dl>

Arguments

Plot r versus LOD grouped by phase — plot_linkage_df

<dl>

<dt>linkage_df</dt>
<dd>A linkage data.frame as output of <code>linkage</code>.</dd>


<dt>r_max</dt>
<dd>Maximum r value to plot</dd>


<dt>stepsize</dt>
<dd>Size of window in recombination frequency to generate mean LOD score. Larger values will reduce plot density.</dd>


<dt>add_legend</dt>
<dd>Logical, should a legend be added to the plot?</dd>


<dt>...</dt>
<dd>Arguments passed to base plot function</dd>

</dl>

plot_linkage_df: Plot r versus LOD grouped by phase

Description

Usage

Arguments

Examples