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.