Plot concordance of -log10 p-values between two methods — plot_pvalue

Creates a scatter plot comparing -log10 transformed p-values from two statistical methods. Optionally colors points by significance and facets by a grouping variable. Correlations and regression lines are shown per facet.

Usage

plot_pvalue_concordance(
  data,
  x_var,
  y_var,
  x_sig_source = NULL,
  y_sig_source = NULL,
  facet_col = NULL,
  facet_levels = NULL,
  x_label = paste("-log10(", x_var, ")"),
  y_label = paste("-log10(", y_var, ")"),
  title = NULL,
  sig_thr = 0.05,
  epsilon = 1e-16,
  log_cap = 5,
  point_size = 0.5
)

Arguments

data: Data frame with p-values and optional grouping/significance.
x_var: Character. Column name for x-axis p-values.
y_var: Character. Column name for y-axis p-values.
x_sig_source: Optional. Column for x significance p-values.
y_sig_source: Optional. Column for y significance p-values.
facet_col: Optional. Column to facet by.
facet_levels: Optional. Levels to include from facet_col.
x_label: Character. X-axis label. Defaults to -log10(x_var).
y_label: Character. Y-axis label. Defaults to -log10(y_var).
title: Character. Optional plot title.
sig_thr: Numeric. P-value threshold for significance. Default 0.05.
epsilon: Numeric. Small value added before log. Default 1e-16.
log_cap: Numeric. Max -log10(p) shown. Default is 5.
point_size: Numeric. Size of points. Default is 0.5.

Value

A ggplot2 object.

Details

Points are shown as -log10(p), capped at log_cap. If significance columns are provided, point color reflects significance source. Faceted plots show correlation (Pearson r) and a regression line.