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UMAP haplotype visualization helper

Source: R/umap_wrapper.R
prepare_hap_umap.Rd

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.