Effect Size Comparison Plot — plot_effect_size

Creates a comparison plot showing effect sizes across traits for pleiotropic SNPs. Helps identify which SNPs have stronger effects on specific traits.

Usage

plot_effect_size_comparison(
  pleio_data,
  top_n_snps = 15,
  effect_col = "PVALUE_MLOG",
  use_log_scale = TRUE,
  show_error_bars = FALSE,
  error_col = NULL,
  color_by = "snp",
  flip_coords = TRUE
)

Arguments

pleio_data: A data.frame containing pleiotropy analysis results
top_n_snps: Integer. Number of top pleiotropic SNPs to include (default: 15)
effect_col: Character. Column to use for effect size (default: "PVALUE_MLOG")
use_log_scale: Logical. Use log scale for effect sizes (default: TRUE)
show_error_bars: Logical. Show error bars (default: FALSE)
error_col: Character. Column for standard errors (default: NULL)
color_by: Character. Color by: "snp", "trait", "chromosome" (default: "snp")
flip_coords: Logical. Flip x and y coordinates (default: TRUE for horizontal bars)

Value

A ggplot2 object

Examples

data(gwas_subset)
pleio_results <- detect_pleiotropy(gwas_subset)
if (nrow(pleio_results) > 0) {
    p <- plot_effect_size_comparison(pleio_results, top_n_snps = 5)
    print(p)
}