NEWS

---

gVenn 1.99.0

New features

• Add a mode argument to computeOverlaps() controlling how genomic intervals are made non-redundant before they are classified. The default, mode = "reduce", keeps the previous "reduce-then-classify" behavior. The new mode = "disjoin" collapses each set on its own, then partitions the union into non-overlapping segments with GenomicRanges::disjoin(), so that every segment is covered by exactly one combination of sets. Because the resulting intervals are merged in one mode and disjoint in the other, the reduced_regions element of GenomicOverlapResult is renamed to regions.
• plotVenn() now attaches eulerr's goodness-of-fit diagnostics (stress, diagError, regionError, undrawnRegions) to the returned plot as a "fit_diagnostics" attribute, and the fit itself as "euler_fit". A message reports diagError and whether it falls above or below the 1e-6 threshold of Micallef and Rodgers (2014), who introduced the measure, and names the populated regions the diagram gives no area to at all, which undrawnRegions records. Set the new verbose = FALSE to silence it.
• Add plotVennError(), which redraws the diagram shaded by the signed error of each region, so the regions a diagram misrepresents can be read off the picture. A thin wrapper around eulerr::error_plot(). It takes the plot returned by plotVenn() as input.
• Add an ignore.strand argument to computeOverlaps()/computeGenomicOverlaps(), passed through to GenomicRanges::reduce(), GenomicRanges::disjoin(), and IRanges::overlapsAny(). Defaults to FALSE (previous, strand-aware behavior is unchanged); set to TRUE to disregard strand when merging or partitioning regions and when determining overlaps.
• computeOverlaps() now warns when two or more input genomic sets share no chromosome name at all, a common symptom of mismatched chromosome naming conventions (e.g. "chr1" vs "1") or of comparing different genome assemblies, cases where overlaps would otherwise be silently and permanently empty. Genome-assembly conflicts on a shared chromosome name already error via GenomicRanges::GRangesList(), unchanged.

Minor updates

• The right-hand annotation of plotUpSet() is now labeled according to the type of the input: "Region size" for a GenomicOverlapResult and "Set size" for a SetOverlapResult.
• computeOverlaps() labels overlap categories faster at large numbers of regions (~10x at 10^5-10^6 regions), by vectorizing the internal defineCategories() helper instead of looping row by row.

Bug fixes

• Fix plotVenn() painting different regions of a four-set diagram in the same color. Since 1.3.2 the palette has been recycled to the number of regions, but it held seven colors against the fifteen regions of a four-set diagram, so eight of them repeated a color. Eight colors were appended. Two- and three-set diagrams draw on the unchanged first seven, so their output is identical.

gVenn 1.3.2

Bug fixes

• Fix plotVenn() failing with fills$fill must have length 1, n_sets, or n_subsets when the data did not populate every region of the diagram. The default fill palette is now recycled to length(fit$original.values) (eulerr's n_subsets), so every region receives a color regardless of which combinations are populated.

gVenn 1.3.1

Bug fixes

• Fix plotVenn() failing on 2-set inputs. The default fill palette had a fixed length of 7, which violated eulerr's stricter validation (fills$fill must have length 1, n_sets, or n_subsets). The default is now recycled to match n_sets.

gVenn 1.1.1

New features

• Add bg parameter to saveViz() for controlling plot background color, including transparent backgrounds. Users can now save plots with bg = "transparent" for use in presentations or publications requiring transparent backgrounds.
• Add hex sticker logo created using the hexSticker R package.
• Update graphical abstract highlighting gVenn's overlap visualization and extraction capabilities

Documentation

• Add example to vignette demonstrating transparent background export using bg = "transparent" parameter in saveViz()

gVenn 0.99.5

Minor update

• Add comb_col parameter to plotUpSet() for customizing the color of combination matrix elements.

Documentation

• Update UpSet plot example in the vignette with color customization of combination matrix elements using the comb_col parameter.

gVenn 0.99.4

New features

• Add exportOverlapsToBed() function to export genomic overlap groups to BED format files.

Documentation

• Updated vignette to include information about exportOverlapsToBed() and guidance on choosing between exportOverlaps() (Excel format) and exportOverlapsToBed() (BED format) based on data type and downstream needs.

gVenn 0.99.3

Minor updates

• Set default colors in plotVenn().

gVenn 0.99.2

New features

• Add customization options for plotVenn().

Documentation

• Improved clarity in function documentation and examples.
• Enhanced vignette with additional customization examples for plotVenn().

gVenn 0.99.1

Minor updates

• Package refinements and documentation improvements for Bioconductor submission.

gVenn 0.99.0

New features

• Initial release of the gVenn package.
• Introduced a workflow for overlap analysis:
  • computeOverlaps() computes intersections across multiple sets of GRanges or gene lists, returning counts and membership categories.
  • extractOverlaps() retrieves the actual elements (regions or genes) that belong to each overlap group for downstream analysis.
  • exportOverlaps() exports overlap groups to an Excel file, creating one sheet per group and converting GRanges to data frames when needed.
• Added visualization functions:
  • plotVenn() to draw proportional Venn diagrams based on overlaps between genomic regions (e.g., ChIP-seq peaks).
  • plotUpSet() to visualize complex overlaps with an UpSet plot.
• Added saveViz() to export visualizations to PDF, PNG, or SVG formats, with optional date tagging in filenames.