Package 'scSpotlight'

Title: A Single Cell Analysis Shiny App
Description: A single cell analysis (viewer) app based on Seurat.
Authors: Zhixia Xiao [aut, cre]
Maintainer: Zhixia Xiao <[email protected]>
License: Apache License (>= 2)
Version: 0.0.5
Built: 2024-11-05 05:52:28 UTC
Source: https://github.com/obenno/scSpotlight

Help Index

Run the scSpotlight App

Description

Run the scSpotlight App

Usage

run_app(
  onStart = set_options,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  dataDir = NULL,
  runningMode = "processing",
  maxSize = 20 * 1000 * 1024^2,
  nCores = 2,
  ...
)

Arguments

onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.
options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.
enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.
uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.
dataDir

Direcotry path of the input data, user could put the large dataset in the direcoty to avoid uploading files
runningMode

The running mode of the app. This could be "processing" (default) or "viewer". The "processing" mode allows users to process input data by Seurat package while in "viewer" mode, user will only be able to view the dimension reduction result and query gene expressions.
maxSize

Maximum allowed total size (in bytes) of global variables identified, see future.globals.maxSize.
nCores

Number of the threads to use (by future::plan()).
...

arguments to pass to golem_opts. See ?golem::get_golem_options for more details.

Examples

## Not run: 
 ## Run app in processing mode
 run_app()

 ## Run app in viewer mode and load data in dataDir
 run_app(runningMode = "viewer", dataDir = "/path/to/data")

 ## Run app on port 8081, shiny::runApp() options need to be wrapped in a list
 run_app(options = list(port = 8081, host ="0.0.0.0", launch.browser = FALSE), runningMode = "processing")

## End(Not run)