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Heatmap of top differentially methylated sites

Source: R/plot_heatmap.R
plot_heatmap.Rd

Produces a heatmap showing methylation beta values for the top differentially methylated sites across all samples. Sites are ranked by adjusted p-value and ordered vertically by effect size (delta beta) to reveal condition-specific patterns.

Usage

plot_heatmap(results, object, n_sites = 50L, annotation_cols = NULL)

Arguments

results

A data.frame returned by results(), containing at minimum the columns chrom, position, strand, mod_type, dm_padj, and dm_delta_beta.

object

A commaData object that was used to produce results. Used to extract the methylation matrix for selected sites.

n_sites

Positive integer. The number of top sites (ranked by ascending dm_padj) to include in the heatmap. If fewer significant (non-NA padj) sites exist, all are shown. Default 50.

annotation_cols

Character vector naming columns from sampleInfo(object) to display as a colored annotation bar above the heatmap. If NULL (default), the condition column is used.

Value

A ggplot object. The x-axis shows sample names; the y-axis shows the selected sites (y-axis labels suppressed for readability). The fill color encodes methylation beta (blue = 0, white = 0.5, red = 1). NA values are shown in light grey. An annotation strip below shows sample-level metadata encoded by color.

See also

diffMethyl, results, plot_volcano

Examples

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


# Show only top 20 sites
plot_heatmap(res, cd_dm, n_sites = 20)