startEpiviz: Start the epiviz interface

In epiviz/epivizr-release: R Interface to epiviz web app

Description

Create an epiviz session manager which can be used to add and delete tracks and plots in the browser web app.

Usage

  startEpiviz(port = 7312L, localURL = NULL, useDevel = FALSE, standalone=FALSE, 
    staticSitePath = "", chr = "chr11", start = 99800000, end = 103383180, 
    debug = FALSE, workspace = NULL, scripts=NULL, gists=NULL, openBrowser = TRUE,
    daemonized = .epivizrCanDaemonize(), verbose = FALSE, 
    nonInteractive = FALSE, tryPorts = FALSE)

Arguments

port	(integer) port for websocket server
localURL	(character) use this url for the epiviz server instead of the standard URL (http://epiviz.cbcb.umd.edu). For example localURL="http://localhost/epiviz" when serving from the local host
useDevel	(logical) use the devel branch of the epiviz server (http://epiviz-dev.cbcb.umd.edu)
standalone	(logical) run the epiviz app on localhost using the httpuv http server
staticSitePath	(character) location of standalone epiviz static site directory. Uses the "www" directory of the installed package by default (i.e., when staticSitePath==""
chr	(character) chromosome to browse to on startup
start	(integer) start position to browse to on startup
end	(integer) end position to browse to on startup
debug	(logical) start the epiviz browser in debug mode
workspace	(character) a workspace id to load in the epiviz web app on startup
scripts	(character vector) URLs for JavaScript plugin scripts to be imported when epiviz is loaded (see http://epiviz.cbcb.umd.edu/help for details).
gists	(character vector) Ids for github gists (http://gist.github.com) containing JavaScript plugin scripts to be imported when epiviz is loaded (see http://epiviz.cbcb.umd.edu/help for details).
openBrowser	(logical) browse to the epiviz URL before exiting function
daemonized	(logical) use non-blocking version if available (UNIX-like platforms only)
verbose	(logical) display log messages on websocket requests
nonInteractive	(logical) run in non-interactive mode, for development purposes only
tryPorts	(logical) try more ports if port number given by argument port is in use.

Value

an object of class EpivizDeviceMgr.

Author(s)

Hector Corrada Bravo

See Also

EpivizDeviceMgr-class

Examples

## Not run: 
mgr <- startEpiviz(openBrowser=FALSE)
mgr$startServer()
mgr$stopServer()

## End(Not run)

epiviz/epivizr-release documentation built on May 16, 2019, 8:18 a.m.