Template-class: BrowserVizDemo: Interactive R/browser plotting

In paul-shannon/igv-ngl: igvNgl: explore relations between DNA variants and protein structure

Description

An early, simple example of how to create useful interactive graphics in a class derived from BrowserViz. This package could evolve to be a drop-in replacement for the R base "plot" function, for plotting xy values. It has the additional virtue of full interactivity on the plotting surface, which is here an HTML5/d3 canvas. Manually selected points on that canvas, for example, can be queried in R. This may facilitate exploratory data analysis.

Usage

BrowserVizDemo(portRange, host="localhost", title="BrowserVizDemo", quiet=TRUE)

## S4 method for signature 'BrowserVizDemoClass'
plot(obj, x, y)
## S4 method for signature 'BrowserVizDemoClass'
getSelection(obj)

Arguments

obj	The BrowserVizDemoClass object returned by the class constructor.
x	A numeric vector, the x-coordinates of the points to plot.
y	A numeric vector, the y-coordinates of the points to plot.
portRange	One or more consecutive integers in the range 1025-65535. A typical choice is 9000:9024. The BrowserViz class constructor will try these one at a time in succession until a free port is found and the connection to your web browser is established. If no open ports are found in the supplied range, an error is reported.
host	Nearly always left to its default value, "localhost" but included as a parameter supporting remote computers for future flexibility.
title	The constructor creates a new window (or a new tab, depending on how you web browser is configured). This title is displayed at the top of the window or tab.
quiet	Trace and tracking messages are written to the R console if this variable is set to FALSE.

Methods

In the code snippets below, obj is an instance of the BrowserVizDemoClass.

BrowserVizDemo(portRange, host="localhost", title="BrowserVizDemo", quiet=TRUE, browserFile=NA): Constructs a BrowserVizDemo object. Among the several actions included are: your default webrowser browses to the uri of a minimal http server embedded in BrowserVizDemo; the browserFile is returned to the browser; the websocket connection is initialized on both ends, and the lowest numbered port in portRange.

plot(obj, x, y): Draws an interactive xy plot in your browser window, with labeled axes, and the surface scaled to the x and y coordinates. In time this method will mimic the rich behavior of the base R plot method, and all of its optional parameters.

Author(s)

Paul Shannon

Examples

  library(BrowserVizDemo)
    
  plotter <- BrowserVizDemo(4000:4024)

  ## make sure everything is ready to use
  while(!ready(plotter)) Sys.sleep(0.1)

  ## plot a simple set of x-y paris
  plot(plotter, 1:10, (1:10)^2)


  ## learn which port we are using
  port(plotter)  

  ## illustrate a "low level" call.  This detail is usually hidden from
  ## the user, implemented and contained (in the case of this example)
  ## in a getWindowTitle(plotter) method call.  This level of detail
  ## reveals what goes on behind the scenes.

  msg <- list(cmd="getWindowTitle", status="request", callback="handleResponse", payload="")
  send(plotter, msg)
  while(!browserResponseReady(plotter)) Sys.sleep(0.1)
  getBrowserResponse(plotter)

  ## a simpler user-level approach:
  getBrowserWindowTitle(plotter)

  ## set and get the windowTitle
  setBrowserWindowTitle(plotter, "new title")
  getBrowserWindowTitle(plotter)

  ## BrowserVizDemo provides another information method which, like the others, will apply
  ## and maybe be of some use to derived classes 
  getBrowserWindowSize(plotter)

  ## finally, you should close BrowserVizDemo when you are done, returning
  ## the port for use by other applications.
  closeWebSocket(plotter)

paul-shannon/igv-ngl documentation built on May 27, 2019, 7:46 a.m.