Add gene labels to a Manhattan plot — manhattan

A convenience wrapper that annotates a dataset and then creates a Manhattan plot with gene names as labels instead of SNP IDs.

Usage

manhattan_genes(
  data,
  genes,
  gene_p_threshold = 1e-05,
  gene_top_n = 10,
  gene_max_distance = 5e+05,
  arrow = FALSE,
  arrow_color = "grey30",
  label_size = 3,
  label_face = "italic",
  ...
)

Arguments

data: A gwas_data object or data.frame with GWAS results.
genes: Gene annotation data.frame (see annotate_genes()).
gene_p_threshold: P-value threshold for gene annotation.
gene_top_n: Number of top genes to label.
gene_max_distance: Maximum distance to nearest gene.
arrow: If TRUE, use annotation arrows instead of text labels.
arrow_color: Color of annotation arrows.
label_size: Font size for gene labels.
label_face: Font face for gene labels ("italic", "bold", "bold.italic").
...: Additional arguments passed to manhattan_plot().

Value

A ggplot object.

Examples

data(example_gwas)
genes <- data.frame(
  chr = c(1, 2, 5, 7, 11), start = c(1e6, 50e6, 80e6, 30e6, 60e6),
  end = c(2e6, 52e6, 85e6, 35e6, 65e6),
  gene = c("BRCA1", "FTO", "TCF7L2", "CDKAL1", "KCNQ1")
)
manhattan_genes(example_gwas, genes = genes, gene_top_n = 5)