plot_genoprobcomp: Plot comparison of two sets of genotype probabilities

Description

Plot a comparison of two sets of genotype probabilities for one individual on one chromosome, as a heat map.

Usage

plot_genoprobcomp(
  probs1,
  probs2,
  map,
  ind = 1,
  chr = NULL,
  geno = NULL,
  threshold = 0,
  n_colors = 256,
  swap_axes = FALSE,
  ...
)

Value

None.

Arguments

probs1: Genotype probabilities (as produced by calc_genoprob()) or allele dosages (as produced by genoprob_to_alleleprob()).
probs2: A second set of genotype probabilities, just like probs1.
map: Marker map (a list of vectors of marker positions).
ind: Individual to plot, either a numeric index or an ID.
chr: Selected chromosome to plot; a single character string.
geno: Optional vector of genotypes or alleles to be shown (vector of integers or character strings)
threshold: Threshold for genotype probabilities; only genotypes that achieve this value somewhere on the chromosome (in one or the other set of probabilities) will be shown.
n_colors: Number of colors in each color scale.
swap_axes: If TRUE, swap the axes, so that the genotypes are on the x-axis and the chromosome position is on the y-axis.
...: Additional graphics parameters passed to graphics::image().

Details

We plot the first set of probabilities in the range white to blue and the second set in the range white to red and attempt to combine them, for colors that are white, some amount of blue or red, or where both are large something like blackish purple.

Examples

Run this code

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[228,"1"]   # subset to one individual on chr 1
map <- insert_pseudomarkers(iron$gmap, step=5)

# introduce genotype error and look at difference in genotype probabilities
pr_ne <- calc_genoprob(iron, map, error_prob=0.002)
iron$geno[[1]][1,2] <- 3
pr_e <- calc_genoprob(iron, map, error_prob=0.002)

# image of probabilities + comparison
old_mfrow <- par("mfrow")
par(mfrow=c(3,1))
plot_genoprob(pr_ne, map, main="No error")
plot_genoprob(pr_e, map, main="With an error")
plot_genoprobcomp(pr_ne, pr_e, map, main="Comparison")
par(mfrow=old_mfrow)