Changelog

Source: NEWS.md

gghic 0.2.1

Major Changes

• S4 Method System for Hypergraphs: Converted hypergraph construction workflow from S3 to S4 methods for better type safety and extensibility.
  • buildHypergraph() is now a generic S4 method build() with methods for MultiWayContacts objects.
  • tidyHypergraph() replaced with S4 generic tidy() method.
  • selectHypergraph() replaced with S4 generic select() method.
  • All methods support method dispatch on MultiWayContacts class.
  • Maintains backward compatibility through consistent API design.
  • Added show() method for MultiWayContacts class providing informative object summaries.

Documentation Improvements

• Comprehensive Documentation Overhaul: Significantly enhanced roxygen2 documentation across all user-facing functions.
  • Added detailed @details sections explaining algorithms, workflows, and technical considerations.
  • Expanded @param descriptions with valid options, defaults, and usage guidance.
  • Included 8-12 practical examples per major function covering common use cases.
  • Added @seealso cross-references linking related functions.
• Enhanced Function Documentation:
  • geom_hic(): Added coordinate system explanation, transformation details, scaling algorithms.
  • geom_loop() and geom_loop2(): Detailed BEDPE format specification, styling options.
  • geom_tad() and geom_tad2(): Comprehensive boundary visualization guidance.
  • geom_track() and geom_track2(): File format support, scaling strategies, comparison table.
  • geom_annotation(): Gene model visualization, GTF parsing, style comparison.
  • geom_concatemer() and geom_concatemer2(): Multi-way contact representation.
  • geom_hypergraph(): Network visualization workflow and layout algorithms.
  • geom_ideogram(): Cytogenetic band display, genome assembly support.
  • geom_hic_under(): Inverted heatmap visualization for comparative displays.
  • scaleData(): Transformation functions (log, asinh, sqrt) with mathematical formulas.
  • All S4 classes and methods: Comprehensive slot descriptions and usage examples.

Bug Fixes

• Fixed unresolved roxygen2 link in setters-methods.R (changed [import()] to [import-ChromatinContacts]).

Internal Changes

• Improved consistency in function naming and parameter conventions.
• Enhanced code organization for hypergraph workflow methods.

gghic 0.2.0

Major Changes

• ChromatinContacts S4 Class: Introduced a new S4 class for managing Hi-C/-like data with improved object-oriented design.
  • New import() methods for loading data from Cooler files.
  • Setter methods for assigning genomic features (TADs, loops, tracks, compartments).
  • Comprehensive subsetting methods supporting numeric, logical, character, GRanges, and GInteractions indexing.
  • Enhanced show() method for better object summaries.

New Features

• Multi-way Contact Visualization: Added geom_hypergraph() for visualizing Pore-C/-like multi-way chromatin interactions.
• Lower Triangle Plots: New geom_hic_under() for plotting flipped Hi-C heatmaps below the diagonal.
• Resolution Depth Analysis: Implemented C-based resolution depth calculation with caching support for improved performance.
• Pairs File Support: Added readPairsCache() for reading and caching pairs files with filtering capabilities.
• Concatemer Conversion: New concatemers2Gis() function to convert concatemer reads to GInteractions.

Performance Improvements

• Implemented C code for resolution depth calculations with hash table-based bin tracking.
• Added comprehensive caching system for resolution and depth calculations.
• Memory-efficient pairs file I/O with filtering support.

Documentation

• Added comprehensive hypergraph vignette for multi-way contact analysis.
• Enhanced main vignette with improved workflow examples and data loading.
• Refactored depth vignette with better caching explanations.
• Updated pkgdown website with better navigation and feature descriptions.

Enhancements

• Refactored all geom_* functions for consistent parameter handling.
• Added renameGeomAes() utility for remapping ggplot2 aesthetics (source: https://github.com/clauswilke/relayer).
• Better error messages and validation throughout.

Internal Changes

• Refactored utility functions with consistent naming conventions.
• Added Makevars with compiler flags for C code compilation.

gghic 0.1.0

• Added core functionalities for visualising genomic interaction data.
• Integrated with ggplot2 for flexible and customisable plotting.
• Included support for heatmaps, chromosome ideograms, gene tracks, and other genomic data tracks.