genotype_plot: Genotype Plotting

In JimWhiting91/genotype_plot: Visualises Genotypes Within a VCF File Located Somewhere on the System, or Loaded as a vcfR Object

Description

Visualises genotypes within a VCF file located somewhere on the system, or loaded as a vcfR object

Usage

genotype_plot(
  vcf = NULL,
  chr = NULL,
  start = 0,
  end = NULL,
  popmap = NULL,
  cluster = FALSE,
  snp_label_size = 1e+05,
  colour_scheme = c("#FCD225", "#C92D59", "#300060"),
  vcf_object = NULL,
  invariant_filter = TRUE,
  is.multi_allelic = FALSE,
  is.haploid = FALSE,
  polarise_genotypes = NULL,
  plot_allele_frequency = FALSE,
  plot_phased = FALSE,
  missingness = 0.5
)

Arguments

vcf	Path to a bgzipped vcf as a character string.
chr	Chr of scaf ID as a character string.
start	Start of region as numeric/integer.
end	End of region as numeric/integer.
popmap	Two column data frame with column 1 for individual IDs as they appear in the VCF and column 2 for pop labels.
cluster	Logical TRUE/FALSE whether to organise haplotypes by hclust clustering.
snp_label_size	Physical distance between snp label markers as numeric/integer.
colour_scheme	Character vector of colour values, must be length 3.
vcf_object	A vcfR object to plot, specified as an alternative to vcf, chr, start and end.
invariant_filter	Logical TRUE/FALSE to remove invariants.
is.multi_allelic	Logical TRUE/FALSE to handle multi-allelic VCFs.
is.haploid	Logical TRUE/FALSE to handle haploid genotypes.
polarise_genotypes	Character string that matches a population in the popmap, genotypes are polarised to the major allele in this population.
plot_allele_frequency	Logical TRUE/FALSE to switch on/off plotting per-population allele frequencies.
plot_phased	Logical TRUE/FALSE to determine whether we plot genotypes or phased haplotypes.
missingness	Numeric between 0-1 to filter for missing genotypes.

Value

A list of plottable objects including genotypes, SNP labels, dendrogram

JimWhiting91/genotype_plot documentation built on Feb. 1, 2022, 9:22 p.m.