Changelog

Source: NEWS.md

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.