Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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() Changes in version 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. Changes in version 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. Changes in version 0.99.3 Minor updates - Set default colors in plotVenn(). Changes in version 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(). Changes in version 0.99.1 Minor updates - Package refinements and documentation improvements for Bioconductor submission. Changes in version 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.