Selective sweep scan plots — geom

Plot selective sweep scan statistics along chromosomes or selected genomic regions. Supports common selscan outputs such as iHS, nSL, iHH12, XP-EHH, and XP-nSL tables, plus XPCLR window tables imported with import_selection().

Usage

geom_selection(
  mapping = ggplot2::aes(x = .data$pos/1e+06, y = .data$value),
  data = NULL,
  ...,
  stat = "all",
  chr = NULL,
  start = NULL,
  end = NULL,
  geom = c("point", "line"),
  colour_by = c("stat", "chr"),
  value = c("signed", "absolute"),
  threshold = NULL,
  threshold_type = c("value", "quantile"),
  threshold_color = "#D55E00",
  threshold_linetype = "dashed",
  size = NULL,
  alpha = NULL,
  base_size = 11,
  base_family = "",
  palette = "publication",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

plot_selection(
  data,
  stat = "all",
  chr = NULL,
  start = NULL,
  end = NULL,
  geom = "point",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  base_size = 11,
  base_family = "",
  palette = "publication",
  value = c("signed", "absolute"),
  threshold = NULL,
  threshold_type = c("value", "quantile"),
  style = c("auto", "single", "manhattan"),
  binary = FALSE,
  threshold_color = "#D55E00",
  threshold_linetype = "dashed",
  point_size = NULL,
  point_alpha = NULL,
  ...
)

Arguments

mapping: Aesthetic mapping. Defaults to position in Mb and selection score.
data: A ggpop_selection object from import_selection().
...: Additional geom parameters.
stat: Selection statistic names to plot, e.g. c("ihs", "xpehh") or "all".
chr: Optional chromosome vector.
start, end: Optional genomic region boundaries in base pairs.
geom: Draw "point" or "line" layers.
colour_by: Colour by statistic or chromosome.
value: Plot signed scores or absolute scores. Absolute mode replaces value with abs(value) and draws only positive threshold lines.
threshold: Optional threshold. With threshold_type = "value", this is a score cutoff such as 2. With threshold_type = "quantile", values between 0 and 1 are interpreted as quantile probabilities such as 0.95.
threshold_type: Interpret threshold as fixed score values or quantile probabilities. Quantiles are computed from absolute scores after statistic, chromosome, and region filtering.
style: Direct plot layout. "auto" uses a Manhattan-like chromosome axis unless chr, start, or end is supplied; local calls use the single-region position axis. Use "manhattan" or "single" to force a layout.
binary: Use two alternating chromosome colours for Manhattan-like selection plots. The default "manhattan" palette alternates #4E79A7 and #C4E2F3.
threshold_color, threshold_linetype: Threshold line appearance.
size, alpha: Layer appearance for geom_selection().
point_size, point_alpha: Point appearance for plot_selection(). Single-region plots default to smaller points; Manhattan-like plots default to the GWAS Manhattan point style.
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_selection() returns a list of ggplot layers. plot_selection() returns a ggplot object.

Examples

selscan_dir <- system.file("extdata", "selective_sweep", "selscan", package = "ggpop")
selection <- import_selection(selscan_dir, type = "selscan")
#> Error: `dir` must point to an existing directory.
selection |> plot_selection(stat = "ihs", value = "absolute")
#> Error: object 'selection' not found
selection |> plot_selection(stat = c("ihs", "xpehh"), chr = "1")
#> Error: object 'selection' not found
selection |> ggpop() + geom_selection(stat = "ihs", chr = "1", threshold = 2)
#> Error: object 'selection' not found
selection |> plot_selection(stat = "ihs", chr = "1", value = "absolute",
  threshold = 0.95, threshold_type = "quantile")
#> Error: object 'selection' not found