Network Graph Visualization for Pleiotropic SNPs — plot_pleiotropy

Creates an interactive network graph showing connections between pleiotropic SNPs and their associated traits. Nodes represent SNPs and traits, edges represent significant associations.

Usage

plot_pleiotropy_network(
  pleio_data,
  min_n_traits = 2,
  top_n_snps = 10,
  node_size_snp = 5,
  node_size_trait = 8,
  edge_width_max = 3,
  layout = "fr",
  show_labels = TRUE,
  label_size = 3,
  color_palette = "okabe_ito"
)

Arguments

pleio_data: A data.frame containing pleiotropy analysis results
min_n_traits: Integer. Minimum number of traits per SNP to include (default: 2)
top_n_snps: Integer. Number of top pleiotropic SNPs to highlight (default: 10)
node_size_snp: Numeric. Base size for SNP nodes (default: 5)
node_size_trait: Numeric. Base size for trait nodes (default: 8)
edge_width_max: Numeric. Maximum edge width (default: 3)
layout: Character. Layout algorithm: "fr", "kk", "dh", "grid", "circle" (default: "fr")
show_labels: Logical. Show node labels (default: TRUE)
label_size: Numeric. Label font size (default: 3)
color_palette: Character. Color palette: "okabe_ito", "viridis", "default" (default: "okabe_ito")

Value

A ggraph ggplot2 object

Examples

data(gwas_subset)
pleio_results <- detect_pleiotropy(gwas_subset)
if (nrow(pleio_results) > 0) {
    p <- plot_pleiotropy_network(pleio_results, top_n_snps = 5)
    print(p)
}
#> Warning: Unknown or uninitialised column: `SNP`.
#> Warning: Unknown or uninitialised column: `SNP`.
#> Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps