startEpiviz: Start the epiviz interface

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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  startEpiviz(port = 7312L, localURL = NULL, useDevel = FALSE,
    chr = "chr11", start = 99800000, end = 103383180, debug = FALSE,
    proxy = TRUE, workspace = NULL, scripts=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)

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

proxy

(logical) start the epiviz browser using the data proxy. This is useful when hosting the web app locally, but want to use data hosted in the epiviz server

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

openBrowser

(logical) browse to the epiviz URL before exiting function

daemonized

(logical) use non-blocking version if available

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

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

## End(Not run)

epiviz/epivizr-tmp documentation built on May 16, 2019, 8:19 a.m.