ChemoSpec: plotSpectraJS – R documentation

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plotSpectraJS

Plot a Spectra Object Interactively

Description

This function uses the d3.js JavaScript library by Mike Bostock to plot a Spectra object interactively. This is most useful for data exploration. For high quality plots, consider plotSpectra.

Usage

plotSpectraJS(spectra, which = NULL, browser = NULL, minify = TRUE)

Arguments

`spectra`	An object of S3 class `Spectra` to be checked.
`which`	Integer. If not `NULL`, specifies by number which spectra to plot. If greater control is needed, use `removeSample` which is more flexible before calling this function.
`browser`	Character. Something that will make sense to your OS. Only necessary if you want to override your system specified browser as understood by `R`. See below for further details.
`minify`	Logical. Shall the JavaScript be minified? This improves performance. However, it requires package `js` which in turn requires package `V8`. The latter is not available on all platforms. Details may be available at https://github.com/jeroen/V8

Details

The spectral data are incorporated into the web page. Keep in mind that very large data sets, like NMR spectra with 32K points, will bog down the browser. In these cases, you may need to limit the number of samples in passed to this function. See removeSample or use argument which.

Value

None; side effect is an interactive web page. The temporary directory containing the files that drive the web page is written to the console in case you wish to use those files. This directory is deleted when you quit R. If you wish to read the file, don't minify the code, it will be unreadable.

Browser Choice

The browser is called by browseURL, which in turn uses options("browser"). Exactly how this is handled is OS dependent.

RStudio Viewer

If browser is NULL, you are using RStudio, and a viewer is specified, this will be called. You can stop this by with options(viewer = NULL).

Browser Choice (Mac)

On a Mac, the default browser is called by /bin/sh/open which in turn looks at which browser you have set in the system settings. You can override your default with browser = "/usr/bin/open -a 'Google Chrome'" for example.

Browser Choice & Performance

You can check the performance of your browser at peacekeeper.futuremark.com The most relevant score is the rendering category.

Author(s)

Bryan A. Hanson, DePauw University.

Examples

if (interactive()) {
  require("jsonlite")
  require("js")
  data(metMUD2)
  plotSpectraJS(metMUD2)
}

ChemoSpec

Exploratory Chemometrics for Spectroscopy

v5.3.11

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)

Initial release

2021-03-24