ggplot_onegeno {qtl2ggplot}

Plot one individual's genome-wide genotypes

Description

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)

# plot the inferred genotypes for the first four individuals
ggplot_onegeno(geno, map, ind=1:4)