build_right_phenoplot

build_right_phenoplot() builds a horizontal plot displaying the mean
difference in phenotype score between individuals with the alternate vs
reference alleles for each SNP locus, grouped by marker group, coloured by
the alternate allele frequency of each SNP. Makes use of the $Varfile
phenotypic information from haplotyping object. It 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_right_phenoplot 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

Right SNP-pheno phenoplot — build_right_phenoplot

<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_right_phenoplot: Right SNP-pheno phenoplot

Description

Usage

Value

Arguments

Examples