Plot concordance of -log10 p-values between two methods

Creates a scatter or hexbin plot comparing -log10 transformed p-values from two statistical methods. Optionally colors points by significance and facets by a grouping variable. Correlation coefficients and regression lines are shown globally or 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,
  title = NULL,
  x_label = NULL,
  y_label = NULL,
  color_label = NULL,
  sig_thr = 0.05,
  log_cap = 5,
  epsilon = 1e-16,
  point_size = 0.5,
  hex = FALSE
)

Arguments

data

Data frame containing p-values and optional grouping or significance columns.

x_var

Character. Name of the column for x-axis p-values.

y_var

Character. Name of the column for y-axis p-values.

x_sig_source

Optional character. Column for significance of x p-values.

y_sig_source

Optional character. Column for significance of y p-values.

facet_col

Optional character. Column name to facet the plot by.

facet_levels

Optional character vector. Subset of levels to include from facet_col.

title

Character. Optional plot title.

x_label

Character. X-axis label. Defaults to -log10(x_var).

y_label

Character. Y-axis label. Defaults to -log10(y_var).

sig_thr

Numeric. P-value threshold for calling significance. Default is 0.05.

log_cap

Numeric. Maximum value shown for -log10(p). Default is 5.

epsilon

Numeric. Small constant added before log10 transform. Default is 1e-16.

point_size

Numeric. Size of points in the scatter plot. Default is 0.5.

hex

Logical. If TRUE, use hexagonal binning instead of individual points. Default is FALSE.

Value

A ggplot2 object showing the concordance of p-values between two methods.

Details

If hex = TRUE, a hexbin plot is produced without individual points or significance coloring. Otherwise, a scatter plot is shown with optional significance-based coloring and shape encoding for capped values. Correlation (Pearson's r) and regression lines are shown globally or per facet if faceting is enabled.