GWAS effect-size volcano plot — volcano

Plot effect size (BETA) against statistical significance (-log10(p)), revealing both the magnitude and direction of genetic effects. Unlike RNA-seq volcano plots, this variant can color by chromosome and scale point size by allele frequency.

Usage

volcano_plot(
  data,
  beta = NULL,
  p = NULL,
  snp = NULL,
  p_threshold = 5e-08,
  beta_threshold = NULL,
  color_by = "significance",
  size_by = NULL,
  point_size = 0.8,
  alpha = 0.6,
  label_snps = NULL,
  label_top_n = NULL,
  colors = c(significant = "#E74C3C", nonsignificant = "#BDC3C7"),
  title = NULL
)

Arguments

data: A gwas_data object or data.frame.
beta, p, snp: Column name overrides.
p_threshold: P-value significance threshold.
beta_threshold: Minimum |BETA| to consider significant.
color_by: How to color points: "significance", "chromosome", or a column name.
size_by: Column name to scale point size (e.g. "AF"), or NULL.
point_size: Base point size (used when size_by is NULL).
alpha: Point transparency.
label_snps: Character vector of SNP IDs to label.
label_top_n: Label the top N most significant SNPs.
colors: Named color vector: "significant" and "nonsignificant" for significance mode, or any custom palette.
title: Plot title.

Value

A ggplot object.

Examples

data(example_gwas, package = "ggwas")

# Basic volcano
volcano_plot(example_gwas)


# Label top hits
volcano_plot(example_gwas, label_top_n = 5)


# Color by chromosome
volcano_plot(example_gwas, color_by = "chromosome", label_top_n = 5)


# Scale point size by allele frequency
volcano_plot(example_gwas, size_by = "AF", label_top_n = 3)