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foundrShiny Developer Guide Overview & Architecture

index.Rmd

foundrShiny Developer Guide Overview & Architecture

Package Purpose & Ecosystem

foundrShiny is an R Shiny package providing interactive web applications for analyzing and visualizing multiparent founder study data (such as Attie Lab founder mouse diet and calcium studies). It serves as the modular interactive web companion to the core analytical package foundr (branch foundrBase).

Related packages in the ecosystem: - foundr: Core data analysis algorithms, statistical models, and ggplot2 visualization functions. - foundrShiny: Interactive Shiny module UI wrappers, tab routers, reactive state handlers, and standalone test apps. - foundrHarmony: Data harmonization across multi-tissue study datasets (in development). - modulr: Standardization of WGCNA module objects.

High-Level Module Architecture & Reactivity Flow

The package contains ~30 interconnected Shiny modules organized hierarchically. Below is the complete visual reactivity calling flowchart across the top-level application, panel routers, parameter tiers, and analytical sub-modules.

flowchart TD
    foundrApp["foundrApp / foundrServer"]
    entryServer["entryServer (Auth)"]
    panelServer["panelServer (5-Tab Router)"]

    mainParServer["mainParServer (Global Parameters)"]
    panelParServer["panelParServer (Panel Parameters)"]
    plotParServer["plotParServer (Plot Parameters)"]

    traitServer["traitServer (Trait Panel)"]
    contrastServer["contrastServer (Contrast Panel)"]
    statsServer["statsServer (Stats Panel)"]
    timeServer["timeServer (Time Panel)"]
    aboutServer["aboutServer (About Panel)"]

    corPlotApp["corPlotApp"]
    corTableApp["corTableApp"]
    traitNamesApp["traitNamesApp (x2)"]
    traitOrderApp["traitOrderApp"]
    traitPairsApp["traitPairsApp"]
    traitSolosApp["traitSolosApp"]
    traitTableApp["traitTableApp"]

    contrastGroupApp["contrastGroupApp"]
    contrastTimeApp["contrastTimeApp"]
    contrastTableApp["contrastTableApp (x3)"]
    contrastTraitApp["contrastTraitApp"]
    timePlotApp["timePlotApp"]
    contrastPlotApp["contrastPlotApp"]
    timeTraitsApp["timeTraitsApp"]
    timeTableApp["timeTableApp"]

    biplotApp["biplotApp"]
    dotplotApp["dotplotApp"]
    volcanoApp["volcanoApp"]

    foundrApp --> entryServer
    foundrApp --> panelServer

    panelServer --> mainParServer
    panelServer --> traitServer
    panelServer --> contrastServer
    panelServer --> statsServer
    panelServer --> timeServer
    panelServer --> aboutServer

    %% Trait Panel Sub-modules
    traitServer --> panelParServer
    traitServer --> corPlotApp
    traitServer --> corTableApp
    traitServer --> traitNamesApp
    traitServer --> traitOrderApp
    traitServer --> traitPairsApp
    traitServer --> traitSolosApp
    traitServer --> traitTableApp

    %% Contrast Panel Sub-modules
    contrastServer --> panelParServer
    contrastServer --> contrastGroupApp
    contrastServer --> contrastTimeApp
    contrastServer --> contrastTableApp
    contrastServer --> contrastTraitApp
    contrastServer --> timePlotApp

    contrastGroupApp --> contrastPlotApp
    contrastTableApp --> traitOrderApp
    contrastTimeApp --> timeTraitsApp
    contrastTraitApp --> contrastPlotApp

    contrastPlotApp --> plotParServer
    contrastPlotApp --> biplotApp
    contrastPlotApp --> dotplotApp
    contrastPlotApp --> volcanoApp

    biplotApp --> mainParServer
    biplotApp --> panelParServer
    biplotApp --> plotParServer
    biplotApp --> contrastTableApp

    %% Stats Panel Sub-modules
    statsServer --> panelParServer
    statsServer --> contrastPlotApp

    %% Time Panel Sub-modules
    timeServer --> panelParServer
    timeServer --> timePlotApp
    timeServer --> timeTableApp

    timeTableApp --> timeTraitsApp
    timeTableApp --> traitOrderApp

    classDef entry fill:#1f77b4,stroke:#333,stroke-width:2px,color:#fff
    classDef router fill:#ff7f0e,stroke:#333,stroke-width:2px,color:#fff
    classDef param fill:#2ca02c,stroke:#333,stroke-width:2px,color:#fff
    classDef panel fill:#d62728,stroke:#333,stroke-width:2px,color:#fff
    classDef submod fill:#9467bd,stroke:#333,stroke-width:2px,color:#fff
    classDef plot fill:#8c564b,stroke:#333,stroke-width:2px,color:#fff

    class foundrApp,entryServer entry
    class panelServer router
    class mainParServer,panelParServer,plotParServer param
    class traitServer,contrastServer,statsServer,timeServer,aboutServer panel
    class corPlotApp,corTableApp,traitNamesApp,traitOrderApp,traitPairsApp,traitSolosApp,traitTableApp,contrastGroupApp,contrastTimeApp,contrastTableApp,contrastTraitApp,timePlotApp,contrastPlotApp,timeTraitsApp,timeTableApp submod
    class biplotApp,dotplotApp,volcanoApp plot

Developer Quick Start

Local Development Workflow 

# Load local package sources dynamically
devtools::load_all()

# Re-generate documentation & NAMESPACE
devtools::document()

# Run R package checks
devtools::check()

For detailed information on individual modules, parameters, and data loading routines, explore the sub-guides: