build_top_metaplot

build_top_metaplot() builds a vertical stacked bar plot displaying the
frequency of each haplotype combination, broken down by each categorical
metadata variable provided. Makes use of the $Indfile information from a
haplotype object. This is an in internal function called by crosshap_viz(),
though can be called separately to build a stand-alone plot

A local haplotyping visualization toolbox to capture major patterns
of co-inheritance between clusters of linked variants, whilst connecting findings
to phenotypic and demographic traits across individuals. 'crosshap' enables users
to explore and understand genomic variation across a trait-associated region.
For an example of successful local haplotype analysis, see Marsh et al. (2022)
<doi:10.1007/s00122-022-04045-8>.

Jacob Marsh

crosshap

Local Haplotype Clustering and Visualization

Brady Johnston

Jakob Petereit

build_top_metaplot function

<dl><dt>HapObject</dt>
<dd>Haplotype object created by run_haplotyping()</dd>
<dt>epsilon</dt>
<dd>Epsilon to visualize haplotyping results for.</dd>
<dt>hide_labels</dt>
<dd>If TRUE, legend is hidden.</dd></dl>

Arguments

Top metadata-hap bar plot — build_top_metaplot

<dl>

<dt>HapObject</dt>
<dd>Haplotype object created by run_haplotyping()</dd>


<dt>epsilon</dt>
<dd>Epsilon to visualize haplotyping results for.</dd>


<dt>hide_labels</dt>
<dd>If TRUE, legend is hidden.</dd>

</dl>

build_top_metaplot: Top metadata-hap bar plot

Description

Usage

Value

Arguments

Examples