build_right_clusterplot

build_right_jitterplot() builds a horizontal plot displaying the mean
pairwise R^2 linkage between each SNP and all other SNPs in its marker group,
grouped by marker group, coloured by alternate allele frequency. Makes use of
the $Varfile 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_clusterplot 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 intra-cluster linkage plot — build_right_clusterplot

<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_clusterplot: Right intra-cluster linkage plot

Description

Usage

Value

Arguments

Examples