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Interactive Shiny Application

Source: vignettes/shiny-app.Rmd
shiny-app.Rmd

Launching the app 

library(molpathR)

# Launch with pre-loaded example data
db <- mp_example_db()
mp_run_app(db)

# Or launch empty and upload data in the browser
mp_run_app()

Application tabs

Tab 1: Database

The home tab lets you upload data files or load the example database. It shows summary cards (number of patients, samples, variants, reports) and a table of loaded data sources.

Tab 2: Patients

A searchable, filterable master table of all patients. Click a row to expand a detail panel showing that patient’s samples, variants, clinical data, and survival information. Filters include diagnosis, sex, and age range.

Tab 3: Variants

Interactive variant table with gene, classification, and VAF filters. Includes tabs for the variant landscape plot, mutation spectrum, and VAF distribution. Clicking a variant selects its gene for survival stratification.

Tab 4: Reports

Browse all parsed reports with filters for report type, date range, and patient. Click a row to view the full report text in a detail panel.

Tab 5: Survival

Interactive Kaplan-Meier curves with options for overall or progression-free survival. Stratify by diagnosis, sex, or any gene mutation status. Displays log-rank p-values and median survival statistics. Gene selection from the Variants tab automatically propagates here.

Tab 6: Export

Select which data layers to export (patients, samples, variants, reports, clinical, survival). Choose from CSV, TSV, Excel, or RDS formats. Preview the data before downloading.

Cross-tab interactivity

  • Selecting a patient in Tab 2 filters Tabs 3-5 to that patient
  • Selecting a gene/variant in Tab 3 pre-fills the survival stratification gene

Deployment 

# Deploy to shinyapps.io
rsconnect::deployApp(
  appDir = system.file("shiny", "molpathR", package = "molpathR"),
  appName = "molpathR"
)