Manhattan plot layer — geom

Adds a Manhattan plot as a list of ggplot layers: the data layer, threshold lines, fastman-style scales, and the default module theme. `geom_manha()` is the ggplot extension path paired with direct `plot_manha()`.

Usage

geom_manha(mapping = ggplot2::aes(chr = .data$chr, pos = .data$pos, p = .data$p),
  data = NULL, geom = "point", position = "identity", ..., threshold = 5e-8,
  suggestive = 1e-5, threshold_colour = .gwas_threshold_color(),
  suggestive_colour = .gwas_suggestive_color(),
  threshold_color = NULL, suggestive_color = NULL,
  size = 1.5, shape = 20, speedup = TRUE, logp = TRUE, maxP = 14,
  bybp = FALSE, palette = "manhattan", binary = FALSE, base_size = 11,
  base_family = "", na.rm = FALSE, show.legend = FALSE, inherit.aes = TRUE)

Arguments

mapping: Aesthetic mapping. Defaults to `chr`, `pos`, and `p`.
data: Optional layer data.
geom: Geom used for rendering.
position: Position adjustment.
...: Additional layer parameters.
threshold: Genome-wide p-value threshold line.
suggestive: Suggestive p-value threshold line.
size, shape, speedup: Point appearance and fastman-style duplicate compression.
logp: Transform p-values to `-log10(p)`, following ggpop's internal fastman-style layout.
maxP: Maximum displayed transformed value.
bybp: Display position in Mb rather than combined chromosome scale.
palette: A ggpop palette name or a character vector of hex colours.
binary: If `TRUE`, repeat two colours across chromosomes for a binary alternating Manhattan palette. The default "manhattan" palette already alternates two colours.
base_size: Base font size for the default module theme.
base_family: Base font family for the default module theme.
threshold_colour, suggestive_colour: Reference-line colours. Defaults use the publication palette.
threshold_color, suggestive_color: Compatibility aliases for `threshold_colour` and `suggestive_colour`.
na.rm: Remove missing values.
show.legend: Legend display.
inherit.aes: Inherit plot aesthetics.