GvsA: Plot G vs. A

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Plot G vs. A

Description

Plot marker-based vs. pedigree-based additive relationship coefficients

Usage

GvsA(
  parentage,
  G,
  A,
  filename = NULL,
  thresh.G = Inf,
  thresh.A = 0.5,
  Gmax = NULL,
  Amax = NULL
)

Arguments

parentage	Data frame of individuals to plot, with 3 columns: id,mother,father
G	Genomic relationship matrix
A	Pedigree relationship matrix
filename	Name of PDF file to save the results (optional for one individual)
thresh.G	Threshold above which names are displayed (default Inf)
thresh.A	Threshold above which names are displayed (default 0.5)
Gmax	Upper limit for y-axis for plotting. If NULL, maximum value in G is used.
Amax	Upper limit for x-axis for plotting. If NULL, maximum value in A is used.

Details

Useful for finding and correcting pedigree errors. If the G or A coefficient for an individual exceeds the threshold, its name is displayed in the figure. If parentage contains one individual, by default a ggplot2 variable will be returned, but the result can also be written to file. If multiple individuals are present, a filename is required.

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.