Plot a Manhattan plot from a gwas object

Plot a Manhattan plot from a gwas object

Usage

manhattan(
  gwas,
  output,
  lower_logp_threshold = 3,
  label_top_n = NULL,
  label_strategy = "lead_per_locus",
  label_locus_window_kb = 500,
  italic_gene_labels = TRUE,
  highlight_genes = NULL,
  highlight_color = "red3",
  label_color = "black",
  ...
)

Arguments

gwas

A gwas object containing the data to plot.

output

The output file name.

lower_logp_threshold

The lower threshold for the -log10(p-value) to plot. Default is 3.0.

label_top_n

Integer. If set and a `gene_name` column is present, annotate the top N variants (by p-value) with labels using ggrepel. If `gene_name` is missing, labels fall back to cytoband-like text (e.g., `chr4p16.3`). Default is NULL (no labels).

label_strategy

Label selection mode: `"top_n"` (global top N by p-value) or `"lead_per_locus"` (one lead per locus, then top N). Default `"lead_per_locus"`.

label_locus_window_kb

Locus window size in kilobases used when `label_strategy = "lead_per_locus"`. Default 500.

italic_gene_labels

Logical. If TRUE, gene labels are italicized; cytoband fallback labels remain plain text. Default TRUE.

highlight_genes

Optional character vector of gene symbols to highlight (e.g., novel genes). Matching labels are colored with `highlight_color`.

highlight_color

Color for highlighted labels. Default `"red3"`.

label_color

Color for non-highlighted labels. Default `"black"`.

...

Additional arguments passed to `ggsave`.