Plot one individual's genome-wide genotypes
Plot one individual's genome-wide genotypes
plot_onegeno( geno, map, ind = 1, chr = NULL, col = NULL, na_col = "white", swap_axes = FALSE, border = "black", shift = FALSE, chrwidth = 0.5, ... )
geno |
Imputed phase-known genotypes, as a list of matrices
(as produced by |
map |
Marker map (a list of vectors of marker positions). |
ind |
Individual to plot, either a numeric index or an ID. |
chr |
Selected chromosomes to plot; a vector of character strings. |
col |
Vector of colors for the different genotypes. |
na_col |
Color for missing segments. |
swap_axes |
If TRUE, swap the axes, so that the chromosomes run horizontally. |
border |
Color of outer border around chromosome rectangles. |
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 |
None.
A number of graphics parameters can be passed via .... For
example, bgcolor to control the background color.
These are not included as formal parameters in order to avoid
cluttering the function definition.
# 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$gmap, step=1)
pr <- calc_genoprob(iron, map, error_prob=0.002)
# infer genotypes, as those with maximal marginal probability
m <- maxmarg(pr)
# guess phase
ph <- guess_phase(iron, m)
# plot phased genotypes
plot_onegeno(ph, map, shift=TRUE, col=c("slateblue", "Orchid"))
# this is more interesting for Diversity Outbred mouse data
## Not run:
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/master/DOex/DOex.zip")
DOex <- read_cross2(file)
# subset to individuals labeled "232" and "256"
DOex <- DOex[c("232", "256"), ]
pr <- calc_genoprob(DOex, error_prob=0.002)
# infer genotypes, as those with maximal marginal probability
m <- maxmarg(pr, minprob=0.5)
# guess phase
ph <- guess_phase(DOex, m)
# plot phased genotypes
plot_onegeno(ph, DOex$gmap, shift=TRUE)
plot_onegeno(ph, DOex$gmap, ind="256", shift=TRUE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.