plot_joyplot_frequencies: make a joy plot of the distribution of allele frequencies...

In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

make a joy plot of the distribution of allele frequencies within a region

Description

This function plots the distribution of allele frequencies within a region over time, making use of a 'joyplot'

Usage

plot_joyplot_frequencies(
  frequencies,
  time_points,
  picked_ancestor = "ALL",
  picked_population = 1
)

Arguments

frequencies	A tibble containing four columns: time, location, ancestor, frequency. Typically one of the items returned by create_population_selection or select_population when the user specifies track_frequency.
time_points	A sequence of time points for which the user wants to create the joyplot
picked_ancestor	Default is "ALL", where different colors indicate different ancestors. Alternatively, for clarity, the user can specify a specific ancestral allele, and only that allele is plotted
picked_population	If multiple populations were simulated (in the case of simulate_admixture_migration), which population should be plotted? Default is population_1.

Value

a ggplot object

Examples

s <- 0.01
select_matrix <- matrix(nrow = 1, ncol = 5)
select_matrix[1, ] <- c(0.25, 1.0, 1 + 0.5 * s, 1 + s, 0)

markers <- seq(from = 0.2, to = 0.3, length.out = 100)

selected_pop <- simulate_admixture(
                    module = ancestry_module(number_of_founders = 10,
                                             morgan = 1,
                                             markers = markers),
                    pop_size = 1000,
                    total_runtime = 11,
                    select_matrix = select_matrix)
require(ggplot2)
plot_joyplot_frequencies(frequencies = selected_pop$frequencies,
                         time_points = 0:11,
                         picked_ancestor = "ALL")

# joyplot frequencies returns a ggplot object, so we can
# add extra elements:
plot_joyplot_frequencies(frequencies = selected_pop$frequencies,
                         time_points = 0:11,
                         picked_ancestor = "ALL") +
  ggplot2::xlab("Location") +
  ggplot2::ylab("Generations")

thijsjanzen/GenomeAdmixR documentation built on Feb. 16, 2024, 7:27 p.m.