Trait Co-occurrence Network Visualization — plot_trait_cooccurrence

Creates a network showing how often pairs of traits share pleiotropic SNPs. This helps identify trait clusters and shared biological mechanisms.

Usage

plot_trait_cooccurrence_network(
  pleio_data,
  min_shared_snps = 1,
  top_n_traits = 15,
  node_size = 8,
  layout = "fr",
  show_edge_labels = TRUE,
  color_by = "n_snps"
)

Arguments

pleio_data: A data.frame containing pleiotropy analysis results
min_shared_snps: Integer. Minimum shared SNPs to show edge (default: 1)
top_n_traits: Integer. Number of top traits to include (default: 15)
node_size: Numeric. Base node size (default: 8)
layout: Character. Layout algorithm: "fr", "kk", "dh", "grid", "circle" (default: "fr")
show_edge_labels: Logical. Show shared SNP counts on edges (default: TRUE)
color_by: Character. Color nodes by: "n_snps", "degree", "none" (default: "n_snps")

Value

A ggraph ggplot2 object

Examples

data(gwas_subset)
pleio_results <- detect_pleiotropy(gwas_subset)
if (nrow(pleio_results) > 0) {
    p <- plot_trait_cooccurrence_network(pleio_results, top_n_traits = 5)
    print(p)
}
#> Warning: No trait pairs meet minimum shared SNP criteria