Plots fitted coefficients against the authoritative stored -log10(p)
values using the same group legend, colors, effect-direction symbols, theme,
and annotation style as plot_phewas_manhattan(). Coefficients remain on
their fitted model or link scale. Results containing different effect
measures are separated into free-scale facets, each centered at zero,
because their magnitudes are not directly comparable. Mean differences also
require common outcome units and transformations before their magnitudes can
be compared within a panel.
Usage
plot_phewas_volcano(
x,
significance = "bonferroni",
label = NULL,
highlight = NULL,
category_order = NULL,
x_limit = 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_legend_columns = 5L,
group_wrap_width = 24L,
point_size = 2.2,
base_size = 12,
label_size = base_size
)Arguments
- x
A
phewas_result.- significance
Testing threshold to draw:
"bonferroni","bh", or"none".- label, highlight
Explicit phenotype values to label or ring.
- category_order
Optional character vector giving every plotted group in display order.
- x_limit, y_limit
Optional reviewed axis limits. Limits that clip data or the testing threshold error.
x_limitmust be symmetric around zero.- missing
What to do when selected phenotypes are unavailable.
- title
Optional in-plot title.
- label_mode
Label text: phenotype
description,phenotype, or"both".- top_label_n
Number of strongest associations to label automatically when
labelisNULL. Use zero to disable automatic labels.- label_wrap_width
Approximate characters per label line.
- group_legend_columns
Number of columns in the bottom group legend.
- 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.