LD decay plots — geom_ld

Plot LD decay summaries as point, connected line, or fitted line plots. The x-axis is pairwise distance in kilobases and the y-axis defaults to mean LD \(r^2\), with optional D-prime or combined \(r^2\)/D-prime views. All styles support population colouring through the package-wide pop column. pop_group relabels imported file/sample labels; "point" and "line" keep the imported summaries, while "fit" draws population-level fitted curves.

Usage

geom_ld_decay(
  mapping = ggplot2::aes(x = .data$dist_kb, y = .data$r2),
  data = NULL,
  ...,
  pop = NULL,
  pop_group = NULL,
  style = c("point", "line", "fit"),
  measure = c("r2", "D", "both"),
  colour_by = c("pop", "file"),
  size = NULL,
  alpha = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

plot_ld_decay(
  data,
  pop = NULL,
  pop_group = NULL,
  style = c("point", "line", "fit"),
  measure = c("r2", "D", "both"),
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  base_size = 11,
  base_family = "",
  palette = "population",
  ...
)

Arguments

mapping: Aesthetic mapping. Defaults to pairwise distance in Kb and mean LD \(r^2\).
data: A ggpop_ld_decay object from import_ld_decay().
...: Additional geom parameters.
pop: Optional population labels to keep.
pop_group: Optional population group table or path to the standard two-column sample pop file. File labels are matched through sample, then regrouped by the mapped population labels.
style: Draw raw summary "point" layers, raw connected "line" layers, or population-level fitted "fit" curves.
measure: Plot r^2, D-prime, or both measures together.
colour_by: Colour by population or source file.
size, alpha: Layer appearance. Point plots default to size 1, matching common LD decay summaries.
base_size, base_family: Base theme font controls.
palette: ggpop discrete palette.
na.rm, show.legend, inherit.aes: Standard ggplot2 layer arguments.
title, subtitle, caption: Optional plot labels. No default title is added.

Value

geom_ld_decay() returns a list of ggplot layers. plot_ld_decay() returns a ggplot object.

Examples

ld_dir <- system.file("extdata", "ld_decay", "PopLDdecay_grouped", package = "ggPopi")
groups <- system.file("extdata", "pop_group.txt", package = "ggPopi")
ld <- import_ld_decay(ld_dir, type = "poplddecay", pop_group = groups)
#> Error: `dir` must point to an existing directory.
ld |> plot_ld_decay(style = "point")
#> Error: object 'ld' not found
ld |> plot_ld_decay(style = "line")
#> Error: object 'ld' not found
ld |> plot_ld_decay(style = "fit")
#> Error: object 'ld' not found
ld |> ggpop() + geom_ld_decay(style = "point")
#> Error: object 'ld' not found