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scExploreR app

Source: R/run_scExploreR.R
run_scExploreR.Rd

Initializes the main scExploreR app.

Usage

# Option 1: Single-object deployment with 
# an object and an object config file
run_scExploreR(
 object = "path_to_object",
 config_file = "path_to_config_file.yaml"
 )

# Option 2: Multi-object deployment with
# Browser config file with paths to object, 
# config files for any number of objects
#  
run_scExploreR(
 browser_config = "path_to_browser_config_file.yaml"
 )

Arguments

browser_config

path to a YAML config file giving browser specific settings. For more info on generating this config file, see here.

object_path

path to a single-cell object to be configured. Currently, Seurat, SingleCellExperiment, and anndata objects are supported. For SingleCellExperiment objects with using HDF5 disk-backed storage via HDF5Array, object_path should be a path to the directory containing the se.rds and assays.h5 files for the object.

config_path

path to the config file for the single-cell object. This is generated either in the config app via run_config_app, or by auto-generating a config file via generate_config_yaml and editing it by hand. For more information on using the config app, see here.

enable_metadata_addition

when TRUE, users may interactively add metadata to objects in the app. This feature is currently unstable, so it must be opted in to by setting this value to TRUE.

port

specify a port for launching the browser. This is optional for a single deployment but required to run several instances of the browser at the same IP address. The port can be any number between 3000:8000, except for ports blocked by Google Chrome (for more information on this, see runApp).

host

This is passed to shiny::runApp. See the documentation of host in runApp for more info.

launch_browser

This is passed to shiny::runApp as launch.browser. See the documentation of launch.browser in runApp for more info.

full_stack_trace

when TRUE, the full stack trace of errors is logged to the console (FALSE by default).

dev_mode

used for development and debugging. When this is TRUE, additional logging occurrs, and the status of the app is printed in the UI. This is not reccomended to be used outside of development.

Details

For more information on setting up an scExploreR deployment, see the dataset setup guide on our website.