Volcano Plot

Creates a volcano plot using ggplot2 based on specified x and y variables, highlighting points that exceed significance and effect size thresholds.

Usage

plot_volcano(
  data,
  x_var,
  y_var,
  sig_thr = NULL,
  effect_thr = NULL,
  x_label = NULL,
  y_label = paste0("-log10(", y_var, ")"),
  title = NULL,
  point_size = 0.5
)

Arguments

data

A data frame containing the variables to be plotted.

x_var

A string specifying the name of the column to be used as the x-axis (e.g., effect size or test statistic).

y_var

A string specifying the name of the column to be used for computing -log10(p) on the y-axis (typically a p-value or adjusted p-value).

sig_thr

Optional numeric value specifying the significance threshold for p-values. If NULL, no significance filtering is applied.

effect_thr

Optional numeric value specifying the minimum absolute effect size threshold. If NULL, no effect size filtering is applied.

x_label

Optional string for the x-axis label. If NULL, uses x_var as default.

y_label

Optional string for the y-axis label. Default is paste0("-log10(", y_var, ")").

title

Optional string for the plot title.

point_size

Numeric value for the size of the points in the scatter plot. Default is 0.5.

Value

A ggplot object representing the volcano plot.

Examples

df <- data.frame(
  feature = LETTERS[1:10],
  T_obs = rnorm(10),
  p_value = runif(10),
  p_adj = p.adjust(runif(10))
)
plot_volcano(df, x_var = "T_obs", y_var = "p_adj", sig_thr = 0.05, effect_thr = 1)