Q-Q plot layer for GWAS p-values — geom

Adds a Q-Q plot as a list of ggplot layers using the same core p-value cleaning, truncation, speedup, publication-palette diagonal, and lambda annotation contract as ggpop's internal fastqq-style layout, while applying the tidyplot-style ggpop theme from `theme_tidyplot()`. `geom_qq()` is the ggplot extension path paired with direct `plot_qq()`.

Usage

geom_qq(mapping = ggplot2::aes(p = .data$p), data = NULL, geom = "point",
  position = "identity", ..., size = 0.8, alpha = 0.8, colour = "black",
  diagonal = TRUE, diagonal_colour = .gwas_threshold_color(),
  diagonal_color = NULL, show_lambda = TRUE,
  maxP = 14, fix_zero = TRUE, speedup = TRUE, base_size = 11,
  base_family = "", lambda_size = base_size * 0.65, na.rm = FALSE,
  show.legend = FALSE, inherit.aes = TRUE)

Arguments

mapping: Aesthetic mapping. Defaults to `p`.
data: Optional layer data.
geom: Geom used for rendering.
position: Position adjustment.
...: Additional layer parameters.
na.rm: Remove missing values.
size, alpha, colour: Point appearance for publication style.
diagonal: Draw the expected-equals-observed diagonal.
diagonal_colour: Diagonal line colour. Defaults to the unified ggpop publication threshold colour and can be overridden explicitly.
diagonal_color: Compatibility alias for `diagonal_colour`.
show_lambda: Display genomic inflation factor.
maxP: Maximum displayed `-log10(p)` value, following ggpop's internal fastqq-style layout.
fix_zero: Replace zero p-values with the minimum non-zero p-value before log transform.
speedup: Round expected and observed values to reduce duplicate points, following ggpop's internal fastqq-style layout.
base_size: Base font size for the tidyplot-style ggpop theme.
base_family: Base font family for the tidyplot-style ggpop theme.
lambda_size: Font size for the genomic inflation factor annotation.
show.legend: Legend display.
inherit.aes: Inherit plot aesthetics.