Density–signal dual-track plot — density_signal

Compare SNP genotyping density against association signal strength across the genome. Each chromosome has two rows: the top track shows the number of variants per bin (density), and the bottom track shows the minimum p-value per bin (signal). This helps distinguish genuine association signals from artifacts driven by uneven genotyping or imputation coverage.

Usage

density_signal_plot(
  data,
  chr = NULL,
  bp = NULL,
  p = NULL,
  bin_size = 1e+06,
  chr_info = NULL,
  density_palette = "viridis",
  signal_palette = "magma",
  chromosomes = NULL,
  title = NULL
)

Arguments

data: A gwas_data object or data.frame with GWAS results.
chr, bp, p: Column name overrides.
bin_size: Bin size in base pairs (default 1 Mb).
chr_info: Optional data.frame with chr and length columns. If NULL, chromosome lengths are inferred from the data.
density_palette: Color palette for the density track.
signal_palette: Color palette for the signal track.
chromosomes: Optional integer vector of chromosomes to display.
title: Plot title.

Value

A ggplot object.

Examples

data(example_gwas, package = "ggwas")
density_signal_plot(example_gwas, bin_size = 5e6)


# With chromosome info for accurate lengths
density_signal_plot(example_gwas, bin_size = 5e6,
  chr_info = chr_info_human())


# Subset to specific chromosomes
density_signal_plot(example_gwas, bin_size = 5e6, chromosomes = 1:5)


# Different palettes
density_signal_plot(example_gwas, bin_size = 5e6,
  density_palette = "plasma", signal_palette = "inferno")