Plot a PheWAS Manhattan-style result — plot_phewas

Uses canonical group colors, effect-direction triangles, group separators, directly annotated testing thresholds, boxed labels, and bottom legends. Stored neg_log10_p values remain authoritative, so probabilities that underflowed to zero are still plottable. Group and phenotype order are deterministic.

Usage

plot_phewas_manhattan(
  x,
  significance = "bonferroni",
  label = NULL,
  highlight = NULL,
  category_order = NULL,
  y_limit = NULL,
  missing = c("error", "drop"),
  title = NULL,
  label_mode = c("description", "phenotype", "both"),
  top_label_n = 0L,
  label_wrap_width = 26L,
  group_display = c("legend", "auto", "x_axis"),
  group_legend_columns = 5L,
  group_label_rows = 3L,
  group_wrap_width = 24L,
  point_size = 2.2,
  base_size = 12,
  label_size = base_size,
  axis_break_mode = c("off", "auto", "on"),
  axis_break_top = 55,
  axis_break_top_size = 0.125
)

Arguments

x: A phewas_result.
significance: Any of "bh", "bonferroni", and "none".
label, highlight: Explicit phenotype values to label or ring.
category_order: Optional character vector giving every group in display order. The argument name is retained for API compatibility; plotted metadata use the canonical group field.
y_limit: Optional reviewed limits on the original -log10(p) scale. Limits that clip data or testing thresholds error.
missing: What to do when selected phenotypes are unavailable.
title: Optional in-plot title. NULL leaves room for an external report or slide title.
label_mode: Label text: phenotype description, phenotype, or "both".
top_label_n: Number of automatically selected labels when label is NULL. Significant associations rank first; use zero to disable.
label_wrap_width: Approximate characters per label line.
group_display: Where to show phenotype groups. The default "legend" matches the volcano plot and leaves a numeric phenotype index on the Manhattan x-axis. "auto" uses centered group labels for compact group sets and a legend for crowded group sets; "x_axis" always places group labels on the Manhattan x-axis.
group_legend_columns: Number of columns in the group legend.
group_label_rows: Rows used to dodge group labels on the x-axis.
group_wrap_width: Approximate characters per group-label line.
point_size: Point size in millimetres.
base_size, label_size: Base and association-label font sizes in points.
axis_break_mode: Optional upper-tail compression: "off", "auto", or "on".
axis_break_top: Compression threshold on the original -log10(p) scale.
axis_break_top_size: Fraction of the plotting range allotted above the compression threshold.

Value

A ggplot object with a phewas_audit attribute.