Genome-wide p-value heatmap — pvalue

A compact, binned heatmap of association signals across the genome. Each cell represents a genomic bin colored by the summary statistic (minimum p-value, median, or count of significant variants). Handles 10M+ SNPs efficiently through pre-aggregation.

Usage

pvalue_heatmap(
  data,
  chr = NULL,
  bp = NULL,
  p = NULL,
  bin_size = 1e+06,
  summary_fun = "min",
  palette = "viridis",
  na_color = "grey95",
  threshold = 5e-08,
  chromosomes = NULL,
  title = NULL
)

Arguments

data: A gwas_data object or data.frame.
chr, bp, p: Column name overrides.
bin_size: Bin size in base pairs (default 1 Mb).
summary_fun: How to summarize p-values per bin: "min" (default), "median", or "count_sig" (count of variants below threshold).
palette: Color palette: "viridis", "magma", "inferno", or "plasma".
na_color: Color for empty bins.
threshold: Significance threshold for count_sig mode and for marking significant bins.
chromosomes: Subset of chromosomes to show.
title: Plot title.

Value

A ggplot object.

Examples

data(example_gwas, package = "ggwas")

# Default (viridis)
pvalue_heatmap(example_gwas, bin_size = 10000)


# Magma palette
pvalue_heatmap(example_gwas, bin_size = 10000, palette = "magma")


# Inferno palette
pvalue_heatmap(example_gwas, bin_size = 10000, palette = "inferno")


# Count significant variants per bin
pvalue_heatmap(example_gwas, bin_size = 10000, summary_fun = "count_sig")