NEWS

CGExplorer 0.3.2 (2026-10-09)

Multi-Page Growth Curve PDF Export: Added export_batch_growth_curves_pdf() to export comprehensive, publication-ready growth curve PDFs for all strains across all plates in a batch:
- Generates one page per strain with facet panels for each plate and individual trajectories for replicate wells.
- Controls (WT, Blank, etc.) are rendered first, followed by mutants alphabetically.
- Uses dynamic per-page y-axis scaling with small margins (~8%) fitted to the strain's own data range, preventing blank upper space for slow-growing or low-yield strains.
Batch Overview Export UI: Added a dedicated export card in mod_batch_overview allowing interactive downloading of Raw OD or Corrected OD multi-page growth curve reports with a live Shiny progress indicator.

Data Fidelity (No Normalization):
- Raw OD mode outputs unmodified absorbance readings directly from instrument assays.
- Corrected OD mode performs direct blank subtraction ($OD_{raw} - OD_{blank_median}$) without clipping, ceiling, or artificial floors (e.g. pmax(..., 0.01)). Negative blank-corrected values are preserved accurately.
- Retains all control wells (Blank, Empty) across both modes.

Automated Failure Detection: compute_metrics() now flags plate QC failure if all blank wells are contaminated or if all wild-type (WT) control wells fail to grow.
Manual QC Override: Users can inspect and toggle a plate's status (PASSED / FAILED) directly within the Plate Card interface.
Batch Quarantine: Added validate_batch_plates() to forbid including FAILED plates in downstream batches.
Layout Consistency Enforcement: validate_batch_plates() verifies that all plates within a single batch share an identical 384-well layout.

Intra-Plate Scoring Gating: Dynamic UI validation prevents selecting the intra-plate (NoDrug_Wells) strategy when layouts lack _NoDrug control wells.
Plate Card Recalculation: Plate edits automatically trigger metric and QC recomputation.
Navigation: Restored and activated Batch Overview and Scoring dashboard menu items.

S4 Data Architecture: Core classes Plate, Batch, and persistent container PlateRegistry.
Tecan Reader & Layout Parsing: Built tidy parsers for Tecan OD raw matrix outputs and 96/384-well plate layouts.
Staining Jump Detection: Automatic staining detection (detect_staining_jump()) for crystal violet biofilm assays.
Interactive Shiny Dashboard: Golem-structured modules for plate browsing, batch building, quality control visualization, and chemo-genomic interaction scoring.