Multi-trait Manhattan plot

Overlay results from multiple GWAS traits or studies on a single Manhattan plot. Each trait is shown in a different color and optionally a different shape, enabling visual identification of shared and trait-specific loci (pleiotropy).

Usage

multitrait_manhattan(
  ...,
  chr = NULL,
  bp = NULL,
  p = NULL,
  snp = NULL,
  colors = "nature",
  shapes = NULL,
  point_size = 0.8,
  alpha = 0.7,
  genome_wide = 5e-08,
  suggestive = 1e-05,
  show_legend = TRUE,
  legend_position = "top",
  highlight_shared = TRUE,
  shared_color = "#9B59B6",
  shared_size = 2.5,
  label_shared_n = NULL,
  downsample = TRUE,
  downsample_n = 150000,
  title = NULL
)

Arguments

...

Named gwas_data objects or data.frames. Names are used as trait labels. Alternatively, pass a single named list.

chr, bp, p, snp

Column name overrides applied to all datasets.

colors

Named vector of colors per trait, or a palette name from gwas_palette().

shapes

Named vector of point shapes per trait (integers). If NULL, all use shape 16 (circle).

point_size

Point size (can be a named vector per trait).

alpha

Point transparency.

genome_wide

Genome-wide significance threshold.

suggestive

Suggestive significance threshold.

show_legend

Show trait legend.

legend_position

Legend position.

highlight_shared

Highlight SNPs significant in multiple traits.

shared_color

Color for shared significant SNPs.

shared_size

Size for shared significant SNPs.

label_shared_n

Label top N shared significant SNPs.

downsample

Enable smart downsampling per trait.

downsample_n

Target points per trait.

title

Plot title.

Value

A ggplot object.

Examples

data(example_gwas)
# Simulate two traits
trait1 <- example_gwas
trait2 <- example_gwas
trait2$P <- runif(nrow(trait2))^3
multitrait_manhattan(Trait1 = trait1, Trait2 = trait2)