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Launch the cellreportR Shiny application

Source: R/shiny.R
cr_run_app.Rd

Starts the interactive front-end bundled with the package. The app covers the whole analysis path in one place: point it at a directory of segmented exports (or upload the files), specify or edit the design, review quality control with a per-unit exclusion table, choose a normalisation, estimate effect sizes as a table plus forest plot, and export a report.

Usage

cr_run_app(
  experiment = NULL,
  max_upload_mb = 512,
  launch_browser = interactive(),
  ...
)

Arguments

experiment

Optional cr_experiment to load on start-up. It is validated with cr_validate_experiment() before the app is built and handed to the server through the app object, so no global state is involved. When NULL (default) the app starts empty and offers synthetic example data.

max_upload_mb

Numeric. Maximum upload size per request, in megabytes. Segmented single-cell exports routinely exceed the Shiny default of 5 MB; this argument raises the limit for the duration of the running app and restores the previous value on exit. Default 512 MB.

launch_browser

Whether to open a browser window. Defaults to TRUE in interactive sessions.

...

Further arguments passed to shiny::runApp().

Value

Invoked for its side effect of running the app. Returns whatever shiny::runApp() returns, invisibly.

Details

The user interface, the server and every helper live inside the package namespace, so the app can be driven in-process by shiny::testServer() as well as from a browser. The directory under inst/shiny/cellreportR/ holds the www/ assets and a thin app.R shim for deployment on a Shiny server.

Requires the shiny, bslib, DT and ggplot2 packages, all listed under Suggests. An informative error naming the missing package is raised when any of them is unavailable.

See also

cr_build_experiment(), cr_report()

Examples

if (interactive()) {
  cr_run_app()
}

# Start from an experiment that is already in the session:
exp <- cr_example_experiment(seed = 1, n_cells_per_well = 10)
if (interactive()) {
  cr_run_app(exp)
}