startStandalone: Start a standalone 'epivizr' session.

In epiviz/epivizrStandalone: Run Epiviz Interactive Genomic Data Visualization App within R

Description

Uses the local repository of epiviz JS app to start a standalone epivizr session through the startEpiviz function. The epiviz app requires a list of sequence names and lengths (e.g., chromsome names and lengths) to setup genome browsing. These can be passed in the seqinfo argument or derived from the gene_track argument. The gene_track argument can be used to pass a genome annotation and add a gene track to the epiviz browser. See package vignette for further detail.

Usage

startStandalone(
  gene_track = NULL,
  seqinfo = NULL,
  keep_seqlevels = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  non_interactive = FALSE,
  register_function = epivizr:::.register_all_the_epiviz_things,
  use_viewer_option = FALSE,
  host = "127.0.0.1",
  ...
)

Arguments

gene_track	(OrganismDb) an object of type OrganismDb or TxDb
seqinfo	(Seqinfo) an object of type Seqinfo from which sequence names and lengths are obtained
keep_seqlevels	(character) vector of sequence names to include in the standalone app
chr	(character) chromosome to browse to on app startup.
start	(integer) start location to browse to on app startup.
end	(integer) end location to browse to on app startup.
non_interactive	(logical) run server in non-interactive mode. Used for testing and development.
register_function	(function) function used to initialize actions in epiviz app. Used for testing and development.
use_viewer_option	(logical) run application in viewer defined by getOption("viewer"). This allows standalone app to run in Rstudio's viewer (FALSE by default)
host	(character) host address for application (127.0.0.1 by default)
...	additional arguments passed to startEpiviz.

Value

An object of class EpivizApp

Examples

# see package vignete for example usage
seqinfo <- GenomeInfoDb::Seqinfo(c("chr1","chr2"), c(10,20))
app <- startStandalone(seqinfo=seqinfo, non_interactive=TRUE)
app$stop_app()

epiviz/epivizrStandalone documentation built on May 5, 2021, 4:27 a.m.