Population genomics statistics plots — geom

Plot windowed population genomics summary statistics along a chromosome, selected region, or multiple chromosomes. By default, selected statistics are stacked vertically with an aligned x-axis, following the pixy plotting style.

Usage

geom_stats(
  mapping = ggplot2::aes(x = .data$pos/1e+06, y = .data$value),
  data = NULL,
  ...,
  stat = "all",
  chr = NULL,
  start = NULL,
  end = NULL,
  geom = c("line", "point"),
  colour_by = c("stat", "chr"),
  size = NULL,
  alpha = NULL,
  base_size = 11,
  base_family = "",
  palette = "publication",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

plot_stats(
  data,
  stat = "all",
  chr = NULL,
  start = NULL,
  end = NULL,
  geom = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  base_size = 11,
  base_family = "",
  palette = "publication",
  ...
)

Arguments

mapping: Aesthetic mapping. Defaults to window midpoint in Mb and statistic value.
data: A ggpop_stats object from import_stats().
...: Additional geom parameters.
stat: Statistic names to plot, e.g. c("fst", "pi") or "all".
chr: Optional chromosome vector.
start, end: Optional genomic region boundaries in base pairs.
geom: Draw "line" or "point" layers. plot_stats() chooses line for one chromosome and point for multiple chromosomes.
colour_by: Colour by statistic or chromosome.
size, alpha: Layer appearance. Defaults follow the pixy plotting examples.
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_stats() returns a list of ggplot layers. plot_stats() returns a ggplot object.

Examples

pixy_dir <- system.file("extdata", "Population_genomics_statistics", "pixy", package = "ggpop")
stats <- import_stats(pixy_dir, type = "pixy")
#> Error: `dir` must point to an existing directory.
stats |> plot_stats(stat = c("fst", "pi"), chr = "chr2L")
#> Error: object 'stats' not found
stats |> plot_stats(chr = "chr2L", start = 1, end = 20000)
#> Error: object 'stats' not found
stats |> ggpop() + geom_stats(stat = "all", chr = c("chr2L", "chr3L"))
#> Error: object 'stats' not found