Skip to contents

Enrichment Manhattan plot

Source: R/enrichment-manhattan.R
enrichment_manhattan.Rd

A Manhattan plot with colored overlays for functional genomic annotations. SNPs falling within annotated regions (genes, enhancers, eQTLs, custom categories) are highlighted with distinct colors, connecting GWAS results with functional genomics.

Usage

enrichment_manhattan(
  data,
  annotations,
  chr = NULL,
  bp = NULL,
  p = NULL,
  snp = NULL,
  background_color = "grey75",
  background_alpha = 0.4,
  annotation_colors = NULL,
  annotation_size = 1.5,
  annotation_alpha = 0.9,
  annotation_shape = 16,
  show_legend = TRUE,
  legend_position = "right",
  genome_wide = 5e-08,
  suggestive = 1e-05,
  label_top_n = NULL,
  label_column = "SNP",
  downsample = TRUE,
  downsample_n = 2e+05,
  title = NULL,
  palette = "nature"
)

Arguments

data

A gwas_data object or data.frame.

annotations

A data.frame or list of data.frames with annotation regions. Each must have columns: chr (integer), start, end. Optionally: category (annotation type), name (region label). If a named list, names are used as category labels.

chr, bp, p, snp

Column name overrides.

background_color

Color for non-annotated SNPs.

background_alpha

Transparency of background points.

annotation_colors

Named vector of colors for each annotation category. If NULL, uses a colorblind-friendly palette.

annotation_size

Point size for annotated SNPs.

annotation_alpha

Transparency of annotated SNPs.

annotation_shape

Point shape for annotated SNPs (default 16, circle).

show_legend

Show legend for annotation categories.

legend_position

Legend position.

genome_wide

Genome-wide significance threshold.

suggestive

Suggestive significance threshold.

label_top_n

Label top N annotated significant SNPs.

label_column

Column to use for labels.

downsample

Enable smart downsampling.

downsample_n

Target number of background points.

title

Plot title.

palette

Color palette for annotations (from gwas_palette()).

Value

A ggplot object.

Examples

data(example_gwas)
# Define annotation regions
annot <- data.frame(
  chr = c(1, 2, 5),
  start = c(1e6, 50e6, 100e6),
  end = c(5e6, 55e6, 110e6),
  category = c("Enhancer", "Gene", "eQTL")
)
enrichment_manhattan(example_gwas, annotations = annot)