Main

[sszvetecz]

Summary by CodeRabbit

• New Features
  • Added target_response parameter to customize IC50 prediction levels (e.g., IC25, IC75).
  • Added transform_x parameter for optional log-scale transformation in visualization and bootstrap functions.
  • Enhanced documentation with new usage examples for advanced prediction scenarios.

[coderabbitai]

Caution

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📝 Walkthrough

Walkthrough

Enhancements introduce optional transformation and targeting parameters to IC50 prediction and visualization functions. The transform_x parameter enables conditional log-scale transformation of IC50 estimates and bootstrap outputs; target_response enables IC50 predictions at custom response levels. Changes propagate across prediction pipelines, visualization functions, and documentation.

Changes

Cohort / File(s)	Summary
Bootstrap Functions & IC50 Prediction R/IC50_prediction.R	Added transform_x parameter to bootstrapIC50 and bootstrapIC50LogScale with conditional log10 transformation logic. Updated return lists to include transformed estimates (mean_ic50_transform, ci_lower_transform, ci_upper_transform) when requested. Transformation flag propagated through bootstrap pipelines.
Visualization Functions R/Visualize_Isotonic_Fit.R	Added target_response and transform_x parameters to plotIsotonic and visualizeResponseProtein. Implemented conditional data preparation and IC50 annotation logic based on transform_x (log-scaled vs. raw dose scales). Updated axis labels, confidence interval rendering, and pIC50 labeling to respect transformation state.
Documentation - Function Signatures man/bootstrapIC50LogScale.Rd, man/plotIsotonic.Rd, man/VisualizeResponseProtein.Rd	Updated Rd documentation to declare new parameters: transform_x (bootstrapIC50LogScale, plotIsotonic) and target_response (plotIsotonic, VisualizeResponseProtein) with default values and descriptions.
Documentation - Parameter Reference man/bootstrapIC50.Rd	Minor documentation update to transform_x description, changing "log10(dose + 1)" to "log10(x + 1)" for consistency.
Vignette & Minor Cleanup vignettes/MSstatsResponse.Rmd, R/ExperimentalDesignSimulation.R	Added vignette section with example demonstrating target_response usage for IC25 predictions. Removed outdated comment line from ExperimentalDesignSimulation.R.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Poem

🐰 ✨ The carrot predictions now bloom in two scales,
Transform or not—whatever prevails,
IC25, IC50, any response we seek,
Target the level, and find what's unique! 🎯🧪

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch main

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