PheWAS plot — phewas_plot • ggwas

Visualize one variant tested across many phenotypes, grouped by phenotype category. The standard figure for biobank-scale phenome-wide association studies (UK Biobank, FinnGen, BioBank Japan).

Usage

phewas_plot(
  data,
  p = "p",
  phenotype = "phenotype",
  category = "category",
  beta = "beta",
  p_threshold = 5e-08,
  colors = NULL,
  point_size = 2,
  alpha = 0.8,
  label_top_n = 5,
  label_column = NULL,
  show_categories = TRUE,
  category_label_angle = 45,
  direction_shape = TRUE,
  title = NULL
)

Arguments

data: A data.frame with columns: phenotype, p (p-value), and category (phenotype group). Optional: beta, description.
p: Column name for p-values.
phenotype: Column name for phenotype labels.
category: Column name for phenotype categories.
beta: Column name for effect sizes (used for direction triangles).
p_threshold: Significance threshold line.
colors: Named vector of colors per category, or a palette name.
point_size: Point size.
alpha: Point transparency.
label_top_n: Label the top N most significant phenotypes.
label_column: Column for label text (default: phenotype).
show_categories: Show category labels on x-axis.
category_label_angle: Rotation angle for category labels.
direction_shape: If TRUE and beta is provided, use triangles pointing up (positive) or down (negative) instead of circles.
title: Plot title.

Value

A ggplot object.

Examples

phewas_data <- data.frame(
  phenotype = paste0("Pheno_", 1:50),
  p = 10^(-runif(50, 0, 8)),
  category = rep(c("Metabolic", "Immune", "Neuro", "Cardio", "Other"), 10),
  beta = rnorm(50, 0, 0.2)
)
phewas_plot(phewas_data)