crosshap_viz

crosshap_viz() builds five individual plots using various elements of a
HapObject created by run_haplotyping(). The central dotplot displays
relationship between clusters of linked SNPs (Marker Groups), and distinct
haplotypes present within the population. Vertical plots (top/bottom)
visualize individuals and populations, grouped by haplotype. Horizontal plots
(left/right) visualize SNP information, grouped by Marker Group cluster.

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

crosshap_viz 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>plot_left</dt>
<dd>When plot_left = "allele", SNP allele frequency information
is displayed, when plot_left = "pos", SNP position information is displayed.</dd>
<dt>plot_right</dt>
<dd>When plot_right = "pheno", phenotype associations for SNPs
are displayed, when plot_right = "cluster", internal marker group linkage is
displayed.</dd>
<dt>hide_labels</dt>
<dd>When TRUE, legends from plots are hidden.</dd>
<dt>isolate_group</dt>
<dd>If one or more Metadata groups are 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

Visualize haplotypes — crosshap_viz

<dl>

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


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


<dt>plot_left</dt>
<dd>When plot_left = "allele", SNP allele frequency information
is displayed, when plot_left = "pos", SNP position information is displayed.</dd>


<dt>plot_right</dt>
<dd>When plot_right = "pheno", phenotype associations for SNPs
are displayed, when plot_right = "cluster", internal marker group linkage is
displayed.</dd>


<dt>hide_labels</dt>
<dd>When TRUE, legends from plots are hidden.</dd>


<dt>isolate_group</dt>
<dd>If one or more Metadata groups are 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>

crosshap_viz: Visualize haplotypes

Description

Usage

Value

Arguments