scan_chrom: Plot spectra by clicking on the chromatogram

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

Plot spectra by clicking on the chromatogram

Description

Plot spectra by clicking on the chromatogram

Usage

scan_chrom(
  chrom_list,
  idx,
  lambda,
  plot_spectrum = TRUE,
  peak_table = NULL,
  scale_spectrum = FALSE,
  spectrum_labels = TRUE,
  export_spectrum = FALSE,
  chr = NULL,
  ...
)

Arguments

chrom_list	A list of chromatograms in matrix format (timepoints x wavelengths). If no argument is provided here, the function will try to find the chrom_list object used to create the provided peak_table.
idx	Numerical index of chromatogram you wish to plot.
lambda	The wavelength to plot the trace at.
plot_spectrum	Logical. Whether to plot the spectrum or not.
peak_table	The peak table (output from get_peaktable function).
scale_spectrum	Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.
spectrum_labels	Logical. If TRUE, plots labels on maxima in spectral plot. Defaults to TRUE.
export_spectrum	Logical. If TRUE, exports spectrum to console. Defaults to FALSE.
chr	Deprecated. Please use idx instead.
...	Additional arguments.

Value

If export_spectrum is TRUE, returns the spectrum as a data.frame with wavelengths as rows and a single column encoding the absorbance (or normalized absorbance, if scale_spectrum is TRUE) at each wavelength. Otherwise, there is no return value.

Side effects

Plots a chromatographic trace from the specified chromatogram (idx), at the specified wavelength (lambda) with a dotted red line to indicate the user-selected retention time. The trace is a single column from the chromatographic matrix.

If plot_spectrum is TRUE, plots the spectrum for the specified chromatogram at the user-specified retention time. The spectrum is a single row from the chromatographic matrix.

Author(s)

Ethan Bass

See Also

Other visualization functions: boxplot.peak_table(), mirror_plot(), plot.peak_list(), plot.peak_table(), plot_all_spectra(), plot_chroms(), plot_spectrum()

Examples

data(Sa_pr)
scan_chrom(Sa_pr, lambda = "210", idx = 2, export_spectrum = TRUE)

ethanbass/chromatographR documentation built on April 17, 2025, 10:55 a.m.