Plot one individual's genome-wide genotypes

Usage

ggplot_onegeno(
  geno,
  map,
  ind = 1,
  chr = NULL,
  col = NULL,
  shift = FALSE,
  chrwidth = 0.5,
  ...
)

Arguments

geno: Imputed phase-known genotypes, as a list of matrices (as produced by maxmarg) or a list of three-dimensional arrays (as produced by guess_phase).
map: Marker map (a list of vectors of marker positions).
ind: Individual to plot, either a numeric index or an ID (can be a vector).
chr: Selected chromosomes to plot; a vector of character strings.
col: Vector of colors for the different genotypes.
shift: If TRUE, shift the chromosomes so they all start at 0.
chrwidth: Total width of rectangles for each chromosome, as a fraction of the distance between them.
...: Additional graphics parameters

Value

object of class ggplot.

Examples

# load qtl2 package for data and genoprob calculation
library(qtl2)

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)

# inferred genotypes
geno <- maxmarg(probs)

# plot the inferred genotypes for the first individual
ggplot_onegeno(geno, map, shift = TRUE)
#> Warning: Some ind not in cross: X
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the qtl2ggplot package.
#>   Please report the issue at
#>   <https://github.com/byandell-sysgen/qtl2ggplot/issues>.


# plot the inferred genotypes for the first four individuals
ggplot_onegeno(geno, map, ind=1:4)
#> Warning: Some ind not in cross: X