% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot_onegeno.R
\name{plot_onegeno}
\alias{plot_onegeno}
\title{Plot one individual's genome-wide genotypes}
\usage{
plot_onegeno(
  geno,
  map,
  ind = 1,
  chr = NULL,
  col = NULL,
  na_col = "white",
  swap_axes = FALSE,
  border = "black",
  shift = FALSE,
  chrwidth = 0.5,
  ...
)
}
\arguments{
\item{geno}{Imputed phase-known genotypes, as a list of matrices
(as produced by \code{\link[=maxmarg]{maxmarg()}}) or a list of
three-dimensional arrays (as produced by \code{\link[=guess_phase]{guess_phase()}}).}

\item{map}{Marker map (a list of vectors of marker positions).}

\item{ind}{Individual to plot, either a numeric index or an ID.}

\item{chr}{Selected chromosomes to plot; a vector of character strings.}

\item{col}{Vector of colors for the different genotypes.}

\item{na_col}{Color for missing segments.}

\item{swap_axes}{If TRUE, swap the axes, so that the chromosomes run horizontally.}

\item{border}{Color of outer border around chromosome rectangles.}

\item{shift}{If TRUE, shift the chromosomes so they all start at 0.}

\item{chrwidth}{Total width of rectangles for each chromosome, as a
fraction of the distance between them.}

\item{...}{Additional graphics parameters}
}
\value{
None.
}
\description{
Plot one individual's genome-wide genotypes
}
\section{Hidden graphics parameters}{

A number of graphics parameters can be passed via \code{...}. For
example, \code{bgcolor} to control the background color.
These are not included as formal parameters in order to avoid
cluttering the function definition.
}

\examples{
# load data and calculate genotype probabilities
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron["146", ] # subset to individual 146
map <- insert_pseudomarkers(iron$gmap, step=1)
pr <- calc_genoprob(iron, map, error_prob=0.002)

# infer genotypes, as those with maximal marginal probability
m <- maxmarg(pr)

# guess phase
ph <- guess_phase(iron, m)

# plot phased genotypes
plot_onegeno(ph, map, shift=TRUE, col=c("slateblue", "Orchid"))

# this is more interesting for Diversity Outbred mouse data
\dontrun{
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
# subset to individuals labeled "232" and "256"
DOex <- DOex[c("232", "256"), ]
pr <- calc_genoprob(DOex, error_prob=0.002)

# infer genotypes, as those with maximal marginal probability
m <- maxmarg(pr, minprob=0.5)
# guess phase
ph <- guess_phase(DOex, m)

# plot phased genotypes
plot_onegeno(ph, DOex$gmap, shift=TRUE)
plot_onegeno(ph, DOex$gmap, ind="256", shift=TRUE)
}

}
