run_dseqr: Run dseqr app

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Run dseqr app

Description

Run dseqr application to explore single-cell and bulk RNA-seq datasets.

Usage

run_dseqr(
  user_name,
  data_dir,
  tabs = c("Single Cell", "Bulk Data", "Drugs"),
  pert_query_dir = file.path(data_dir, ".pert_query_dir"),
  pert_signature_dir = file.path(data_dir, ".pert_signature_dir"),
  gs_dir = file.path(data_dir, ".gs_dir"),
  indices_dir = file.path(data_dir, ".indices_dir"),
  tx2gene_dir = file.path(data_dir, ".tx2gene_dir"),
  app_dir = system.file("app", package = "dseqr", mustWork = TRUE),
  host = "0.0.0.0",
  port = 3838,
  logout_url = NULL,
  is_local = is.null(logout_url),
  test = FALSE,
  is_example = FALSE
)

Arguments

user_name	Name of user folder in data_dir. Will be created if doesn't exist.
data_dir	Directory containing user folders. By default also will contain folders .pert_query_dir, .pert_signature_dir, and .indices_dir.
tabs	Character vector of tabs to include in order desired. Must be subset of 'Single Cell', 'Bulk Data', and 'Drugs'.
pert_query_dir	Path to directory where pert query results (using CMAP02/L1000 as query signature) will be downloaded as requested.
pert_signature_dir	Path to directory where pert signatures for CMAP02/L1000 will be downloaded as requested.
gs_dir	Path to directory where gene to Gene Ontology maps produced by get_genego are saved.
indices_dir	Path to directory containing kallisto indices and whitelists.
tx2gene_dir	Path to directory containing transcript to gene maps produced by load_tx2gene.
app_dir	Directory containing shiny app files. Default is to use 'app' directory of installed dseqr package. Can be 'inst/app' if working from source code.
host	The IPv4 address that the application should listen on. Defaults to the shiny.host option, if set, or "127.0.0.1" if not. See Details.
port	The TCP port that the application should listen on. If the port is not specified, and the shiny.port option is set (with options(shiny.port = XX)), then that port will be used. Otherwise, use a random port between 3000:8000, excluding ports that are blocked by Google Chrome for being considered unsafe: 3659, 4045, 5060, 5061, 6000, 6566, 6665:6669 and 6697. Up to twenty random ports will be tried.
logout_url	URL used to log users out. Default is NULL for local use.
is_local	Is dseqr running locally? If FALSE, uses CDNs for some dependencies and sets up other dseqr.com specific tags. Default is TRUE if logout_url is NULL, otherwise FALSE.
test	Create a test with shinytest2? Default is FALSE.
is_example	Is the app for demonstration purposes? If TRUE, various features are disabled to prevent dataset changes.

Value

Runs dseqr app

Examples

if (interactive()) {

  data_dir <- tempdir()
  user_name <- 'example'
  run_dseqr(user_name, data_dir)
}

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.