NEWS
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.