crosshap_viz {crosshap}

Visualize haplotypes

Description

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.

Usage

crosshap_viz(
  HapObject,
  epsilon,
  plot_left = "allele",
  plot_right = "pheno",
  hide_labels = FALSE,
  isolate_group = NA
)

Arguments

HapObject

Haplotype object created by run_haplotyping().

epsilon

Epsilon to visualize haplotyping results for.

plot_left

When plot_left = "allele", SNP allele frequency information is displayed, when plot_left = "pos", SNP position information is displayed.

plot_right

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

hide_labels

When TRUE, legends from plots are hidden.

isolate_group

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.

Value

A patchwork object.