Locus zoom plot — locus

Create a regional association plot centered on a genomic region or lead SNP, with optional LD coloring and gene annotation track.

Usage

locus_plot(
  data,
  chr = NULL,
  bp = NULL,
  p = NULL,
  snp = NULL,
  region_chr = NULL,
  region_start = NULL,
  region_end = NULL,
  lead_snp = NULL,
  flank = 5e+05,
  ld = NULL,
  ld_colors = c("#2166AC", "#67A9CF", "#78C679", "#F4A582", "#D73027"),
  ld_breaks = c(0, 0.2, 0.4, 0.6, 0.8, 1),
  gene_data = NULL,
  gene_height = 0.25,
  point_size = 2,
  lead_snp_shape = 23,
  lead_snp_size = 4,
  title = NULL
)

Arguments

data: A gwas_data object or data.frame.
chr, bp, p, snp: Column name overrides.
region_chr: Chromosome of the region to plot.
region_start, region_end: Start and end positions.
lead_snp: SNP ID to center the region around.
flank: Flank size in bp around the lead SNP (default 500kb).
ld: Named numeric vector of LD (r2) values with the lead SNP. Names are SNP IDs, values are r2.
ld_colors: Colors for LD bins (5 levels).
ld_breaks: Breaks for LD color bins.
gene_data: A data.frame with columns: chr, start, end, gene, strand.
gene_height: Proportion of plot height for the gene track.
point_size: Point size.
lead_snp_shape: Shape for the lead SNP marker.
lead_snp_size: Size for the lead SNP marker.
title: Plot title.

Value

A ggplot object (or patchwork composition if gene_data is provided).

Examples

data(example_gwas, package = "ggwas")
locus_plot(example_gwas, region_chr = 1,
           region_start = 1e6, region_end = 20e6)