[Core Logic] Shifted to a Physical-First landscape philosophy. The network layout now defaults to alpha = 0.75, giving 75% weight to physical protein composition to preserve biological specificity and sub-complex architecture.
[Interactive Layer] Replaced all static plotting functions (visualizeMapDirectLabels, visualizeMapWithLegend) with a high-performance interactive engine based on Cytoscape.js and Shiny.
[S3 Object] Overhauled the print.ComplexMap method to provide a “Systems Biology Dashboard” highlighting Functional Diversity, Annotation Coverage, and Physical Density.
[Clustering] Updated functional clustering in generateNodeAttributes to use Average Linkage and a dynamic scaling factor to force functional diversity and prevent “monochromatic” maps.
Improvements
[Export] Enhanced toCytoscapeJSON with coordinate scaling and edge pruning to optimize browser performance for large networks.
[Export]exportNetwork now supports GraphML and sanitizes R-specific data types for Cytoscape Desktop compatibility.
[Documentation] Fully documented missing arguments (layout_seed, ...) and updated vignettes to reflect the v2.0 API.
Bug Fixes
[Metrics] Fixed a critical indexing error in evaluateComplexes where the Maximum Matching Ratio (MMR) would return NA when predicted and reference lists differed in size.
[CRAN] Eliminated non-ASCII characters in complexmap_S3.R and qcComplexList.R to ensure cross-platform portability.
[Architecture] Fixed a corrupt lazy-load database issue by ensuring consistent namespace exports.
ComplexMap 1.1.2 (2026-02-11)
Added
[createComplexMap] Added ifRefineCpx parameter (default: FALSE). Step 1 (Complex Refinement) is now conditional, allowing users to process raw input lists without automatic merging.
Changed
[generateNodeAttributes] Enforced a strict 1:1 mapping between Primary Function and Node Color. Removed the weighted color blending logic to ensure visual consistency across the functional landscape.
[Logging] Updated verbose messaging to explicitly state refinement status during the workflow.
ComplexMap 1.1.1 (2025-12-02)
Major Improvements
[Parallelism] Refactored evaluateComplexes to use future.apply instead of parallel::mclapply, enabling reliable multi-core computation on Windows.
[Workflow] Improved summarizeThemes() to accept add_to_object = TRUE, allowing theme metadata to be stored directly within the S3 object.
Bug Fixes
[Dependencies] Moved clue from Suggests to Imports to ensure the Hungarian algorithm is always available for MMR calculation.
[UI] Fixed a runtime error in the interactive viewer when the color.by argument was null.
[Vignettes] Resolved build failures in vignette_02-workflow.Rmd caused by incorrect internal function calls.
ComplexMap 1.1.0 (2025-11-15)
Added
[Benchmarking] Introduced benchmarkParameters() to systematically optimize mergeThreshold values against reference complexes.
[Metrics] Added dice and matching_score similarity options to refineComplexList.
[Quantitative] Added support for a color.by argument in visualization functions to map continuous experimental data to node colors.
Changed
[Defaults] Updated the default similarityMethod in refineComplexList to "matching_score".
[Traceability]refineComplexList now returns a mergeMap tibble for reproducibility.
[QC] Overhauled qcComplexList output to provide a formatted diagnostic report instead of raw R output.
[Terminology] Renamed the "overlap" similarity metric to "simpson" for scientific accuracy.
ComplexMap 1.0.0 (2025-10-10)
Initial stable release.
Introduced the ComplexMap S3 object for structured proteomics workflows.