SNP density karyogram — snp

Visualize the distribution of genotyped or imputed variants across chromosomes. Two rendering styles are available: "heatmap" (default) bins variants and colors tiles by count, while "points" draws individual variant positions on chromosome outlines — density is visible through natural clustering. Optionally marks centromere positions when chr_info is provided.

Usage

snp_density(
  data,
  chr = NULL,
  bp = NULL,
  p = NULL,
  style = c("heatmap", "points"),
  bin_size = 1e+06,
  color_by = c("density", "significance", "uniform"),
  chr_info = NULL,
  palette = "viridis",
  point_size = 0.3,
  point_alpha = 0.5,
  show_centromeres = TRUE,
  downsample_n = 2e+05,
  title = NULL
)

Arguments

data: A gwas_data object or data.frame with GWAS results.
chr, bp, p: Column name overrides.
style: Rendering style: "heatmap" for binned density tiles, or "points" for individual variant positions on chromosome outlines.
bin_size: Bin size in base pairs (default 1 Mb). Only used when style = "heatmap".
color_by: For style = "points": how to color dots. "density" (default) colors by local density, "significance" colors by -log10(p), or "uniform" for a single color.
chr_info: Optional data.frame with columns chr, length, and optionally centromere_start, centromere_end. Use chr_info_human() for hg38. If NULL, chromosome lengths are inferred from the data.
palette: Color palette: "viridis", "magma", "inferno", or "plasma".
point_size: Point size for style = "points".
point_alpha: Point transparency for style = "points".
show_centromeres: If TRUE and centromere positions are available in chr_info, draw centromere markers.
downsample_n: Maximum number of points to plot in "points" style. Set to NULL to plot all variants (can be slow for >500k).
title: Plot title.

Value

A ggplot object.

Examples

data(example_gwas, package = "ggwas")

# Heatmap style (default)
snp_density(example_gwas, bin_size = 5e6, chr_info = chr_info_human())


# Different palette
snp_density(example_gwas, bin_size = 5e6, palette = "magma",
  chr_info = chr_info_human())


# Points style — individual variants on chromosome outlines
snp_density(example_gwas, style = "points", chr_info = chr_info_human())


# Points colored by significance
snp_density(example_gwas, style = "points", color_by = "significance",
  chr_info = chr_info_human())


# Uniform color, no centromeres
snp_density(example_gwas, style = "points", color_by = "uniform",
  show_centromeres = FALSE)