Heatmap Visualization for SNP-Trait Associations — plot_pleiotropy

Creates a publication-ready heatmap showing -log10(p-value) associations between pleiotropic SNPs and traits. Useful for visualizing patterns of shared genetics.

Usage

plot_pleiotropy_heatmap(
  pleio_data,
  top_n_snps = 20,
  top_n_traits = 10,
  value_col = "PVALUE_MLOG",
  show_dendrograms = FALSE,
  clustering_method = "complete",
  color_palette = "bluered",
  scale = "none",
  show_values = FALSE,
  value_format = NULL,
  legend_title = NULL
)

Arguments

pleio_data: A data.frame containing pleiotropy analysis results
top_n_snps: Integer. Number of top pleiotropic SNPs to include (default: 20)
top_n_traits: Integer. Number of top traits to include (default: 10)
value_col: Character. Column to use for heatmap values (default: "PVALUE_MLOG")
show_dendrograms: Logical. Show row and column dendrograms (default: FALSE)
clustering_method: Character. Clustering method: "complete", "average", "ward.D2" (default: "complete")
color_palette: Character. Color palette: "bluered", "viridis", "plasma", "default" (default: "bluered")
scale: Character. Scale values: "none", "row", "column" (default: "none")
show_values: Logical. Show numeric values in cells (default: FALSE)
value_format: Character. Format string for values (default: NULL)
legend_title: Character. Legend title (default: NULL)

Value

A ggplot2 heatmap object

Examples

data(gwas_subset)
pleio_results <- detect_pleiotropy(gwas_subset)
if (nrow(pleio_results) > 0) {
    p <- plot_pleiotropy_heatmap(pleio_results, top_n_snps = 5, top_n_traits = 4)
    print(p)
}
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the pleior package.
#>   Please report the issue at <https://github.com/danymukesha/pleior/issues>.