prepare_hap_umap: UMAP haplotype visualization helper

In crosshap: Local Haplotype Clustering and Visualization

UMAP haplotype visualization helper

Description

prepare_hap_umap() builds a large composite ggplot2 object ready for faceting and animation (see vignette) for visualizing SNP alleles (coloured by Marker Group) possessed by individuals with each haplotype. UMAP coordinates for each SNP can be generated using umap::umap(), with the LD matrix generated for run_haplotyping() as input. When fully rendered and faceted, the resultant GIF intuitively visualizes the shared loci within each Marker Group that are constant within each haplotype combination.

Usage

prepare_hap_umap(
  umap_in,
  hetmiss_as = "allele",
  HapObject,
  epsilon,
  vcf,
  nsamples = 25
)

Arguments

umap_in	UMAP results produced for a haplotype object at a given epsilon.
hetmiss_as	If hetmiss_as = "allele", heterozygous-missing SNPs './N' are recoded as 'N/N', if hetmiss_as = "miss", the site is recoded as missing.
HapObject	Haplotype object created by run_haplotyping().
epsilon	Epsilon matching the haplotype object used for umap_in.
vcf	Input vcf.
nsamples	Number of times to sample each haplotype group, will directly translate to the number of frames in animation. Should be the same as the nframes passed to gganimate::animate().

Value

A large ggplot2 object.

crosshap documentation built on May 29, 2024, 1:13 a.m.