Launch GateLabR with the canonical GateLab React interface

Starts the shared GateLab TypeScript/React application with a thin Shiny adapter for a SingleCellExperiment. This is the interface started by launchGatingApp, which is the single supported entry point.

Usage

launchReactGateLab(
  sce = NULL,
  sample_column = NULL,
  port = NULL,
  launch.browser = TRUE,
  sce_name = NULL,
  agent = NULL,
  blocking = NULL
)

Arguments

sce

A SingleCellExperiment. If NULL, the first SCE in the global environment is used.

sample_column

Optional colData column defining samples. When omitted, common sample columns such as sample_id are detected.

port

Port for Shiny (default: auto-select).

launch.browser

Whether to open a browser window (default: TRUE).

sce_name

Optional name of the global-environment variable that gates, populations and colData are written back to. Defaults to the symbol the caller passed as sce. Delegating wrappers must forward the user's symbol explicitly, because substitute() would otherwise resolve to the wrapper's own parameter name.

agent

Open the tab connected to an agent's relay: TRUE reads the address the relay recorded in ~/.gatelab/agent-relay.json, or give the ws:// address itself. The agent then reads the gating as you see it and proposes gates, which appear in the tab with a badge; saving stays yours. NULL (the default) opens the tab as usual; the Agent menu in the header can connect it later.

blocking

Whether the call returns only when the app stops. NULL (the default) returns at once when the installed Shiny can run an app in the background (shiny::startApp(), Shiny 1.14 and later) and otherwise blocks as before, saying so. FALSE insists on returning at once and is an error with an older Shiny; TRUE blocks.

Value

Invisibly the running app's handle when the call returns at once (its $stop() stops the app, as does gatelabStop), otherwise invisibly NULL once the app has stopped. The app is serviced while R is idle at the prompt, so a long computation pauses it until the prompt returns. While it runs, the console may change the object it was launched on: the app then refuses to save over that change until gatelabSync hands it the console's object. When the app stops with no population memberships stored in the object, or with memberships older than the workspace, a warning says so: the readers (gatelabPopulations, gatelabHierarchy) need an explicit "Save to SCE", which autosaves do not replace.