GWAS plots • ggPopi

ggpop supports Manhattan and Q-Q plots from common GWAS outputs. The intended flow is:

import a typed object;
plot with plot_manha() / plot_qq() or ggpop() + geom_*();
use internal fastman-style Manhattan and Q-Q plotting behavior without an external fastman dependency.

API summary

Task	Direct API	Layer API	Notes
Import GCTA/GEMMA/EMMAX	`import_gwas(file, type = ...)`	-	Returns `ggpop_gwas`
Manhattan	`plot_manha()`	`ggpop(data) + geom_manha()`	Defaults are aligned
Q-Q	`plot_qq()`	`ggpop(data) + ggPopi::geom_qq()`	Use explicit namespace to avoid `ggplot2::geom_qq()`
Backend	internal fastman-style layout	native ggpop stat	Direct wrappers and geoms share one implementation

GCTA example

gwas <- import_gwas(ggpop_extdata("gwas", "gcta.mlma"), type = "gcta")

plot_manha(gwas)

Manhattan plot. Chromosomes are arranged along the x-axis and minus log10 p-values are on the y-axis. Most points sit below the reference lines, while the horizontal suggestive and genome-wide threshold lines show where stronger GWAS signals would stand out.

plot_qq(gwas)

Q-Q scatter plot. Expected minus log10 p-values are on the x-axis and observed minus log10 p-values are on the y-axis. Points follow the red diagonal reference line closely, and a lambda annotation summarizes genomic inflation.

Layered workflow

gwas |>
  ggpop() +
  geom_manha()

Manhattan plot from the layered ggplot workflow. Chromosomes are arranged along the x-axis and minus log10 p-values are on the y-axis, with horizontal suggestive and genome-wide threshold lines.


gwas |>
  ggpop() +
  ggPopi::geom_qq()

Q-Q scatter plot from the layered ggplot workflow. Expected minus log10 p-values are on the x-axis and observed minus log10 p-values are on the y-axis, with points compared against a diagonal reference line.

plot_manha(gwas) and ggpop(gwas) + geom_manha() share the same default threshold and suggestive reference lines.

GWAS colour palettes

The GWAS module uses the same unified discrete palette entry as the rest of ggpop. Manhattan plots default to a two-colour alternating chromosome palette:

plot_manha(gwas, palette = "manhattan")

Manhattan plot with a two-colour alternating palette. Adjacent chromosomes alternate between blue and pale blue, preserving the same p-value threshold lines.

To override the Manhattan colours, pass two explicit colours. binary = TRUE keeps the two-colour alternation even when a longer palette is supplied:

plot_manha(
  gwas,
  palette = c("#4E79A7", "#C4E2F3"),
  binary = TRUE
)

Manhattan plot with a two-colour alternating palette. Adjacent chromosomes alternate between the two supplied colours, emphasizing chromosome separation without changing the p-value scale or thresholds.

Reference-line colours continue to use the publication palette by default. Override them with threshold_color and suggestive_color when needed.

Alternative GWAS formats

import_gwas() accepts type = "gcta", type = "gemma", and type = "emmax". GWAS plotting uses ggpop’s internal ggplot implementation in both direct and layered workflows.