Package 'BrowserViz'

Title: BrowserViz: interactive R/browser graphics using websockets and JSON
Description: Interactvive graphics in a web browser from R, using websockets and JSON.
Authors: Paul Shannon
Maintainer: Arkadiusz Gladki <[email protected]>
License: GPL-2
Version: 2.29.0
Built: 2024-11-29 04:08:43 UTC
Source: https://github.com/bioc/BrowserViz

Help Index

Supply the name of a function to call, identified by its key

Description

Supply the name of a function to call, identified by its key

Usage

addRMessageHandler(key, functionName)

Arguments

key

A character string
functionName

A character string

browserResponseReady

Description

browserResponseReady

Usage

## S4 method for signature 'BrowserViz'
browserResponseReady(obj)

Arguments

obj

An object of class BrowserViz

Constructor for BrowserViz

Description

This constructor function:

  • creates the BrowserViz object

  • initializes the httpuv web server

  • prepares that web server to additionally handle websocket traffic

  • loads a "browserFile" - an html/javascript/css web page to communicate with in your web browser

  • opens websocket communication between your R session and your browser

  • installs an optional "httpQueryProcessingFunction" to handle http (non-websocket) requests.

Usage

BrowserViz(
  host = "localhost",
  portRange = 10000:10100,
  title = "BrowserViz",
  browserFile,
  quiet = TRUE,
  httpQueryProcessingFunction = NULL
)

Arguments

host

character The constructor will open an http/websocket port here for web browsers to connect to. localhost by default
portRange

The constructor looks for a free websocket port in this range. 10000:10100 by default
title

Used for the web browser window, "igvR" by default
browserFile

The full path to the bundled html, js and libraries, and css which constitute the browser app
quiet

A logical variable controlling verbosity during execution
httpQueryProcessingFunction

a function, default NULL, provides subclasses with the opportunity to execute code on the http server created here.

Value

An object of the BrowserViZ class

BrowserViz: a base class providing simple, extensible message passing between your R session and your web browser, for interactive data visualization.

Description

Many of the best interactive graphics capabilities available today are written in Javascript and run in a web browser. BrowserViz makes these capabilities available in R, using websockets for message passing back and forth between R and the browser. This class connects your R session to your web browser via websockets, using the R httupv library, which in turn uses the Rook webserver.

BrowserViz is a concrete base class, in that instances can be constructed and run - which we do for testing. The primary use of this BrowserViz is to be subclassed: to facilitate the creation of new browser-based, R-connected interactive graphics capabilities embodied in R packages, written by programmers with some skill in both R and Javascript. Two examples of this can be found in these Bioconductor packages https://bioconductor.org/packages/devel/bioc/html/igvR.html and https://bioconductor.org/packages/devel/bioc/html/RCyjs.html.

Slots

uri

The http location at which this modest webserver runs

port

An integer port number for the http connection

websocketConnection

An environment managed by the httpuv library on our behalf

quiet

Logical varaible controlling verbosity during execution

See Also

BrowserViz

An S4 class to create and manage a modest webserver for websocket message passing between R and Javascript running in your web browser

Close the websocket connection - between your R session and your web browser.

Description

Close the websocket connection - between your R session and your web browser.

Usage

## S4 method for signature 'BrowserViz'
closeWebSocket(obj)

Arguments

obj

An object of class BrowserViz

Route the message coming in from the browser to the appropriate R function.

Description

Route the message coming in from the browser to the appropriate R function.

Usage

dispatchMessage(ws, msg, quiet)

Arguments

ws

a websocket connectin
msg

the JSON-encoded message from the browser
quiet

logical TRUE or FALSE

Ask the browser to display html markup in the specified div

Description

Ask the browser to display html markup in the specified div

Usage

## S4 method for signature 'BrowserViz'
displayHTMLInDiv(obj, htmlText, div.id)

Arguments

obj

An object of class BrowserViz
htmlText

A character string with HTML markup
div.id

A character string

Transform JSON string into a native R object

Description

Transform JSON string into a native R object

Usage

fromJSON(...)

Arguments

...

Extra arguments passed to this function

Value

a native R data structure

Examples

fromJSON(toJSON(data.frame(a=8:10, b=LETTERS[8:10], stringsAsFactors=FALSE)))

Retrieve basic attributes of the attached web browser.

Description

Retrieve basic attributes of the attached web browser.

Usage

## S4 method for signature 'BrowserViz'
getBrowserInfo(obj)

Arguments

obj

An object of class BrowserViz

Retrieve the response sent by the browser

Description

Retrieve the response sent by the browser

Usage

## S4 method for signature 'BrowserViz'
getBrowserResponse(obj)

Arguments

obj

An object of class BrowserViz

Supply the name of a function to call, identified by its key

Description

Supply the name of a function to call, identified by its key

Usage

## S4 method for signature 'BrowserViz'
getBrowserWindowSize(obj)

Arguments

obj

An object of class BrowserViz

Supply the name of a function to call, identified by its key

Description

Supply the name of a function to call, identified by its key

Usage

## S4 method for signature 'BrowserViz'
getBrowserWindowTitle(obj)

Arguments

obj

An object of class BrowserViz

handleResponse

Description

handleResponse

Usage

handleResponse(ws, msg)

Arguments

ws

websocket connection
msg

the JSON-encoded character string returned by the browser

Get the port number

Description

Get the port number

Usage

## S4 method for signature 'BrowserViz'
port(obj)

Arguments

obj

An object of class BrowserViz

Value

the port number use in the websocket connection, a numeric value.

Is the websocket connection to the browser ready for use?

Description

Is the websocket connection to the browser ready for use?

Usage

## S4 method for signature 'BrowserViz'
ready(obj)

Arguments

obj

An object of class BrowserViz

Send data to the browser, ensure that it is returned accurately.

Description

Send data to the browser, ensure that it is returned accurately.

Usage

## S4 method for signature 'BrowserViz'
roundTripTest(obj, ...)

Arguments

obj

An object of class BrowserViz
...

other arguments

Send the specified message to the browser

Description

Send the specified message to the browser

Usage

## S4 method for signature 'BrowserViz'
send(obj, msg)

Arguments

obj

An object of class BrowserViz
msg

A list with four fields: cmd: "someCommand", status: "request", callback: "someFunction", payload: "someData"

Supply the name of a function to call, identified by its key

Description

Supply the name of a function to call, identified by its key

Usage

## S4 method for signature 'BrowserViz'
setBrowserWindowTitle(obj, newTitle)

Arguments

obj

An object of class BrowserViz
newTitle

A character string

Display the core attributes of the BrowserViz object to stdout

Description

Display the core attributes of the BrowserViz object to stdout

Usage

## S4 method for signature 'BrowserViz'
show(object)

Arguments

object

An object of class BrowserViz

Transform an R data structure into JSON

Description

The semantics of toJSON changed between RJSONIO and jsonlite: in the latter, scalars are promoted to arrays of length 1. rather than change our javascript code, and since such promotion – while sensible in the context of R – strikes me as gratuitous, I follow jeroen ooms suggestion, creating this wrapper

Usage

toJSON(..., auto_unbox = TRUE)

Arguments

...

Extra arguments passed to this function
auto_unbox

Logical

Value

a character string with the JSON representation of the R object

Examples

toJSON(data.frame(a=8:10, b=LETTERS[8:10], stringsAsFactors=FALSE))

Pause for the specified number of milliseconds

Description

Pause for the specified number of milliseconds

Usage

## S4 method for signature 'BrowserViz'
wait(obj, msecs)

Arguments

obj

An object of class BrowserViz
msecs

Numeric

Is there a web browser available for testing?

Description

This package's unit tests require a web browser to connect to. our heuristic, though not bullet proof, is that one of three conditions must be met Supply the name of a function to call, identified by its key

Usage

webBrowserAvailableForTesting()

Value

Logical TRUE or FALSE