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Interactive Identification of Emission Lines

Source: R/line_finder.R
line_finder.Rd

Launches a Shiny app to identify the emission lines of LIBS spectra. Elements are selected on a periodic table, and the strongest lines of their selected ionization stages, from the NIST Atomic Spectra Database, are overlaid on a spectrum in an interactive plotly graph, with one color per ionization stage.

Usage

line_finder(spectra, launch.browser = interactive(), show_table = TRUE)

Arguments

spectra

Spectra, one per row: a numeric matrix, or a data frame whose wavelength columns are named by their wavelengths (other columns are used as labels).

launch.browser

Passed to shiny::runApp(). Default is TRUE when R is interactive.

show_table

A logical: show the periodic table when the app starts (TRUE, default). The Hide table button of the Elements panel hides or shows it at any time; hiding it gives the spectrum the whole height of the window.

Value

Called for its side effect: runs the app. Use libs_lines() and plot_lines() for the same results in scripts.

Details

The app offers:

  • a clickable periodic table; elements without lines in the wavelength range of the spectra are grayed out once queried. It can be hidden (Hide table) to enlarge the spectrum, and the selected elements stay listed in the panel header;

  • the ionization stages to show (I, II, III);

  • the plasma temperature and the number of lines per species, which set the lines kept and the height of their markers (relative intensities in local thermodynamic equilibrium, see libs_lines());

  • the wavelength range, a wavelength shift to correct the calibration of the spectrometer, and the spectrum to show: the mean of all spectra, the mean of a group (from the first character or factor column of spectra), or a single spectrum;

  • a download of the displayed lines as CSV, and buttons to save and reload the lines fetched so far, so that a session can continue offline.

Each species is downloaded from NIST once per R session (see nist_lines()); later changes of the settings are computed locally. The zoom of the plot is kept when the lines change.

The app needs the shiny, plotly and bslib packages, and an internet connection for the species not yet fetched.

See also

libs_lines(), plot_lines(), nist_lines()

Author

Christian L. Goueguel

Examples

if (interactive() && rlang::is_installed(c("shiny", "plotly", "bslib"))) {
  data(forageLIBS)
  line_finder(forageLIBS[-(1:14)])
}