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Volcano plot for differential methylation results

Source: R/plot_volcano.R
plot_volcano.Rd

Produces a volcano plot from differential methylation results computed by diffMethyl() and extracted with results(). Sites are colored by significance category based on user-supplied adjusted p-value and delta-beta thresholds.

Usage

plot_volcano(results, delta_beta_threshold = 0.2, padj_threshold = 0.05)

Arguments

results

A data.frame returned by results(), containing at minimum the columns dm_delta_beta (numeric, effect size as beta difference treatment minus control) and dm_padj (numeric, BH-adjusted p-value in \([0, 1]\)).

delta_beta_threshold

Numeric scalar in (0, 1). Sites with |dm_delta_beta| >= delta_beta_threshold AND dm_padj <= padj_threshold are considered significant. Default 0.2.

padj_threshold

Numeric scalar in (0, 1). Adjusted p-value cutoff for significance. Default 0.05.

Value

A ggplot object. The x-axis shows dm_delta_beta (effect size), the y-axis shows -log10(dm_padj) (significance). Sites are colored as "Hypermethylated" (positive delta-beta, significant), "Hypomethylated" (negative delta-beta, significant), or "Not significant". Dashed lines mark the threshold boundaries. Sites with NA adjusted p-value are excluded from the plot.

See also

diffMethyl, results, filterResults

Examples

data(comma_example_data)
cd_dm <- diffMethyl(comma_example_data, ~ condition)
res <- results(cd_dm)
plot_volcano(res)


# Custom thresholds
plot_volcano(res, delta_beta_threshold = 0.3, padj_threshold = 0.01)