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AGENTS.md — qtl2shiny

Context

  • Repository: qtl2shiny — Interactive Shiny web interface for QTL fine mapping and gene exploration with R/qtl2.
  • Key Directories:
    • R/: 90+ Shiny modules and utility functions (xxxApp(), xxxServer(), xxxInput(), xxxUI(), xxxOutput()).
    • inst/qtl2shinyApp/: Standalone Shiny application launcher (app.R) and project registry (projects.csv).
    • inst/doc/: Developer walkthroughs and module architecture (module.md, walkthrough.md, scatter.md).
    • vignettes/devel_guide/: Comprehensive developer guides by analysis feature (index.Rmd, geno.Rmd, hotspot.Rmd, mediate.Rmd, scan.Rmd).
  • Core Data Structures: qtl2shinyData directory structure (FST genotype probabilities, LOCO kinship matrices, SQLite variant & gene annotations, phenotype matrices, and hotspot S3 objects).

Role

Act as an expert R package developer, statistical geneticist, and Shiny systems architect specializing in the R/qtl2 ecosystem.

Action & Verification

  • Package Verification: Run devtools::document(), devtools::test(), and devtools::check().
  • Shiny Reactivity Verification: Test module servers with shiny::testServer() or locally via inst/qtl2shinyApp/app.R.
  • Documentation: Never edit files in man/ directly; update Roxygen comments (#') in R/ and guides in vignettes/.

Format & Conventions

  • Shiny Module Structure: Follow standard xxxApp, xxxServer, xxxInput, xxxUI, xxxOutput pattern with shiny::moduleServer() and shiny::NS().
  • UI Framework: Use bslib (Bootstrap 5) layout primitives (page_navbar(), layout_sidebar(), nav_panel(), card()).
  • Namespacing: Use explicit package prefixes (pkg::func()) for all external dependencies.
  • Phenotype Normalization: Use rankZ() / pheno_rankz() for rank-Z transformations.

Tone & Collaboration

  • Direct, concise, and mathematically rigorous.
  • Provide complete drop-in replacement code blocks and run verification checks locally before reporting completion.