build_left_alleleplot

build_left_alleleplot() builds a horizontal plot displaying mean allelic
frequencies (reference/alternate/missing/heterozygous) of all SNP loci,
grouped by marker group. Makes use of $Varfile information from a HapObject
created by run_haplotyping(). This is an 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_left_alleleplot function

<dl><dt>HapObject</dt>
<dd>Haplotype object created by run_haplotyping().</dd>
<dt>epsilon</dt>
<dd>Epsilon matching the haplotype object used for umap_in.</dd>
<dt>hide_labels</dt>
<dd>If TRUE, legend is hidden.</dd></dl>

Arguments

Left SNP-allele plot — build_left_alleleplot

<dl>

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


<dt>epsilon</dt>
<dd>Epsilon matching the haplotype object used for umap_in.</dd>


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

</dl>

build_left_alleleplot: Left SNP-allele plot

Description

Usage

Value

Arguments

Examples