Package index

Core Data Workflows

Import typed data and start tidy ggplot workflows.

ggpop()

Create a ggplot object from ggpop data

import_gwas()

Import GWAS result files

import_pca() compute_pca()

Import or compute PCA results

import_pop_group()

Import population group labels

import_admix() import_admixture()

Import admixture proportion files

GWAS Plots

Manhattan and Q-Q plots for GCTA, GEMMA, and EMMAX results.

plot_manha()

Publication-oriented Manhattan plots

geom_manha()

Manhattan plot layer

plot_qq()

Publication-oriented GWAS Q-Q plots

geom_qq()

Q-Q plot layer for GWAS p-values

PCA Plots

PLINK/GCTA imports and optional flashpcaR computation.

plot_pca()

Publication-oriented PCA plots

geom_pca()

PCA scatter layer

import_pca() compute_pca()

Import or compute PCA results

Admixture Plots

Narrow user-facing admixture plotting API.

plot_admix() as_pophelper_qlist() plot_admixture_pophelper()

Publication-oriented admixture plots

plot_admix2() geom_admix2()

Pure ggplot-style admixture plots

geom_admix()

Admixture barplot layer

Population Genomics Statistics

Windowed FST, pi, Tajima’s D, and related statistics from pixy or vcftools.

import_stats()

Import population genomics summary statistics

geom_stats() plot_stats()

Population genomics statistics plots

LD Decay

LD decay summaries from PopLDdecay and PLINK pairwise LD files.

import_ld_decay()

Import LD decay results

geom_ld_decay() plot_ld_decay()

LD decay plots

Selective Sweep Scans

Selscan and XPCLR imports with chromosome and region plotting.

import_selection()

Import selective sweep scan results

geom_selection() plot_selection()

Selective sweep scan plots

Introgression

Dsuite local/trio statistics, ADMIXTOOLS f-stat tables, and TreeMix graph summaries.

import_introgression()

Import introgression results

geom_introgression() plot_introgression()

Introgression plots

Ne History

Effective population size histories from PSMC, MSMC2, SMC++, and Stairway Plot 2.

import_ne_history() import_demographic_history()

Import effective population size history

geom_ne_history() plot_ne_history() geom_demographic_history() plot_demographic_history()

Effective population size history plots

Styling

Shared palettes, scales, and publication theme helpers.

new_pop_palette() ggpop_palette() scale_colour_ggpop() scale_color_ggpop() scale_fill_ggpop()

Discrete ggpop population palettes

theme_ggpop_publication() ggpop_palette() scale_fill_ggpop() scale_colour_ggpop()

Publication-oriented ggpop styles

theme_tidyplot() theme_ggplot2() theme_minimal_xy() theme_minimal_x() theme_minimal_y() style_void()

ggpop theme helpers

adjust_font()

Adjust ggpop font settings

Advanced Compatibility

Exported integration hooks and original-package compatibility layers.

plot_admix() as_pophelper_qlist() plot_admixture_pophelper()

Publication-oriented admixture plots

pophelper_functions() pophelper_call() import_pophelper_qlist() pophelper_as_qlist() pophelper_is_qlist() read_pophelper_q() plot_pophelper_q() plot_pophelper_q_multiline() align_pophelper_k() sort_pophelper_q() split_pophelper_q() merge_pophelper_q() join_pophelper_q() tabulate_pophelper_q() summarise_pophelper_q() analyse_pophelper_q() evanno_pophelper_structure() pophelper_distruct_colours() pophelper_verify_grplab()

pophelper compatibility layer