Changelog • gVenn

gVenn 1.3.2

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.

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.

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

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

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

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

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

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.

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.