epivizr (version 1.4.6)

startEpiviz: Start the epiviz interface

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

(integer 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.

See Also

EpivizDeviceMgr-class

Examples

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