Publication-oriented Manhattan plots — plot

High-level publication-oriented Manhattan plot builder. `plot_manha()` and the tidy extension path `ggpop(data) + geom_manha()` share ggpop's internal fastman-style ggplot implementation.

Usage

plot_manha(data, title = NULL, subtitle = NULL, caption = NULL,
  threshold = 5e-8, suggestive = 1e-5,
  threshold_colour = .gwas_threshold_color(),
  suggestive_colour = .gwas_suggestive_color(),
  threshold_color = NULL, suggestive_color = NULL,
  point_size = 1.5,
  point_alpha = 0.9, base_size = 11, base_family = "", legend_position = "none",
  logp = TRUE, maxP = 14, bybp = FALSE, palette = "manhattan",
  binary = FALSE, ...)

Arguments

data: A `ggpop_gwas` object.
title, subtitle, caption: Plot text.
threshold, suggestive: Manhattan reference p-value thresholds.
threshold_colour, suggestive_colour: Reference-line colours. Defaults use the publication palette.
threshold_color, suggestive_color: Compatibility aliases for `threshold_colour` and `suggestive_colour`.
point_size, point_alpha: Point appearance.
base_size, base_family, legend_position: Publication theme settings.
logp, maxP, bybp: Core fastman-style controls forwarded by `plot_manha()` and mirrored by `geom_manha()`.
palette: A ggpop palette name or a character vector of hex colours for Manhattan plots.
binary: If `TRUE`, repeat two palette colours across chromosomes for a binary alternating Manhattan plot. The default "manhattan" palette already alternates two colours.
...: Additional layer or backend arguments.