build_bot_halfeyeplot

build_bot_halfeyeplot() builds a vertical plot displaying the
phenotypic scores for each individual, grouped by haplotype, coloured by
metadata variable. Metadata groups can be isolated using the isolate_groups
argument. Makes use of the $Indfile information from haplotype
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_bot_halfeyeplot 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>
<dt>isolate_group</dt>
<dd>If a Metadata group is provided, all other Metadata
groups will be masked from the plot. NOTE: it does change the summary tables
or marker group phenotype scores.</dd></dl>

Arguments

Bot hap-pheno raincloud plot — build_bot_halfeyeplot

<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>


<dt>isolate_group</dt>
<dd>If a Metadata group is provided, all other Metadata
groups will be masked from the plot. NOTE: it does change the summary tables
or marker group phenotype scores.</dd>

</dl>

build_bot_halfeyeplot: Bot hap-pheno raincloud plot

Description

Usage

Value

Arguments

Examples