r_LOD_plot

<code>r_LOD_plot</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

r_LOD_plot function

<dl><dt>linkage_df</dt>
<dd>A linkage data.frame as output of <code>linkage</code>.</dd>
<dt>plot_main</dt>
<dd>A character string specifying the main title</dd>
<dt>chm</dt>
<dd>Integer specifying chromosome</dd>
<dt>r_max</dt>
<dd>Maximum r value to plot</dd>
<dt>tidyplot</dt>
<dd>If <code>TRUE</code> (by default), an attempt is made to reduce the plot density using hexagonal binning from the <code>ggplot2</code> package. 
This is recommended for large datasets, where the number of pairwise estimates becomes high.</dd>
<dt>nbins</dt>
<dd>The number of bins in each direction, passed to ggplot2::geom_hex. Only used if <code>tidyplot = TRUE</code>. Increasing this number
can lead to slower but more accurate plotting.</dd></dl>

Arguments

Plot r versus LOD — r_LOD_plot

<dl>

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


<dt>plot_main</dt>
<dd>A character string specifying the main title</dd>


<dt>chm</dt>
<dd>Integer specifying chromosome</dd>


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


<dt>tidyplot</dt>
<dd>If <code>TRUE</code> (by default), an attempt is made to reduce the plot density using hexagonal binning from the <code>ggplot2</code> package. 
This is recommended for large datasets, where the number of pairwise estimates becomes high.</dd>


<dt>nbins</dt>
<dd>The number of bins in each direction, passed to ggplot2::geom_hex. Only used if <code>tidyplot = TRUE</code>. Increasing this number
can lead to slower but more accurate plotting.</dd>

</dl>

r_LOD_plot: Plot r versus LOD

Description

Usage

Arguments

Examples