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Plot an UpSet Diagram from Genomic or Set Overlap Results

Source: R/plotUpSet.R
plotUpSet.Rd

This function creates an UpSet plot using the ComplexHeatmap package to visualize intersections across multiple sets. Supports both GenomicOverlapsResult and SetOverlapsResult objects.

Usage

plotUpSet(overlap_object, customSetOrder = NULL, comb_col = "black")

Arguments

overlap_object

A GenomicOverlapsResult or SetOverlapsResult object returned by computeOverlaps.

customSetOrder

Optional. A vector specifying the order of sets to display on the UpSet diagram. The vector should contain either numeric indices (corresponding to the sets in the overlap object) or character names (matching the set names). If NULL (default), sets are displayed in decreasing order of their size (set_size()).

comb_col

Optional. Color(s) for the combination matrix dots and connecting lines. Can be a single color, a vector of colors (recycled to match the number of intersections). Default is "black".

Value

An UpSet plot object generated by ComplexHeatmap::UpSet.

Examples

# Example with gene sets (built-in dataset)
data(gene_list)
res_sets <- computeOverlaps(gene_list)

# Default order (sets sorted by size)
plotUpSet(res_sets)


# Custom color
plotUpSet(res_sets, comb_col = "darkblue")


# Custom order by names
plotUpSet(res_sets, customSetOrder = c("random_genes_C",
                                       "random_genes_A",
                                       "random_genes_B"))


# Example with genomic regions (built-in dataset)
data(a549_chipseq_peaks)
res_genomic <- computeOverlaps(a549_chipseq_peaks)
plotUpSet(res_genomic)