ggPopi

ggPopi provides tidy, publication-oriented ggplot2 workflows for common population-genomics plots. It combines typed import helpers, direct plot_*() functions, and composable ggpop() + geom_*() layers.

Supported modules include GWAS Manhattan and Q-Q plots, PCA, admixture, population statistics, LD decay, selective sweep scans, introgression summaries, and demographic / effective population size histories.

Installation

Install the development version from GitHub:

# install.packages("pak")
pak::pak("WWz33/ggPopi")

Core plotting uses CRAN-available dependencies. Optional integrations use:

• flashpcaR for compute_pca(method = "flashpca");
• pophelper for direct plotQ() compatibility helpers.

Quick Start

library(ggPopi)

gwas <- import_gwas(
  system.file("extdata", "gwas", "gcta.mlma", package = "ggPopi"),
  type = "gcta"
)

plot_manha(gwas)

The same imported object can be used through the layered ggplot extension path:

gwas |>
  ggpop() +
  geom_manha()

Interface

Every module follows the same shape:

1. import_*() reads tool output into a typed data frame.
2. plot_*() returns a complete ggplot object with module defaults.
3. ggpop() + geom_*() provides the same visual grammar inside a ggplot pipeline.

Module	Import	Direct plot	ggplot extension	Guide
GWAS	import_gwas()	plot_manha(), plot_qq()	geom_manha(), geom_qq()	GWAS
PCA	import_pca(), compute_pca()	plot_pca()	geom_pca()	PCA
Admixture	import_admix()	plot_admix(), plot_admix2()	geom_admix(), geom_admix2()	Admixture
Population statistics	import_stats()	plot_stats()	geom_stats()	Stats
LD decay	import_ld_decay()	plot_ld_decay()	geom_ld_decay()	LD decay
Selective sweeps	import_selection()	plot_selection()	geom_selection()	Selection
Introgression	import_introgression()	plot_introgression()	geom_introgression()	Introgression
Demographic / Ne history	import_ne_history(), import_demographic_history()	plot_ne_history(), plot_demographic_history()	geom_ne_history(), geom_demographic_history()	Ne history

Documentation

• Getting started: https://wwz33.github.io/ggPopi/articles/ggPopi.html
• Function reference: https://wwz33.github.io/ggPopi/reference/
• Compatibility helpers: https://wwz33.github.io/ggPopi/articles/guides/compatibility.html

Design

ggPopi keeps the user-facing API small while preserving module-specific visual defaults. Direct plot_*() functions are the reference style, and matching geom_*() layers make those defaults available in ggplot compositions.

Palette and theme helpers such as ggpop_palette(), scale_colour_ggpop(), scale_fill_ggpop(), and theme_tidyplot() provide shared styling across modules.