plot_all_spectra: Plot all spectra for chosen peak.

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

Plot all spectra for chosen peak.

Description

Plot multiple for a given peak in peak table. Wrapper for plot_spectrum.

Usage

plot_all_spectra(
  peak,
  peak_table,
  chrom_list,
  idx = "all",
  chrs = NULL,
  engine = c("base", "ggplot2", "plotly"),
  plot_spectrum = TRUE,
  export_spectrum = TRUE,
  scale_spectrum = TRUE,
  overlapping = TRUE,
  verbose = FALSE,
  what = c("peak", "rt", "idx"),
  ...
)

Arguments

peak	The name of a peak to plot (in character format)
peak_table	The peak table (output from get_peaktable function)
chrom_list	A list of chromatograms in matrix format (timepoints x components). If no argument is provided here, the function will try to find the chrom_list object used to create the provided peak_table.
idx	Vector of chromatograms to plot.
chrs	Deprecated. Please use idx instead.
engine	Which plotting engine to use: base, ggplot2, or plotly.
plot_spectrum	Logical. If TRUE, plots the spectrum of the chosen peak.
export_spectrum	Logical. If TRUE, exports spectrum to console. Defaults to FALSE.
scale_spectrum	Logical. If TRUE, scales spectrum to unit height.
overlapping	Logical. If TRUE, plot spectra in single plot.
verbose	Logical. If TRUE, prints verbose output to console.
what	What to look for. Either peak to extract spectral information for a certain peak, rt to scan by retention time, or idx to scan by numeric index. Defaults to "peak" mode.
...	Additional arguments to plot_spectrum.

Value

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

Side effects

If plot_spectrum is TRUE, plots the spectra for the specified chromatogram (idx) of the given peak. 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_chroms(), plot_spectrum(), scan_chrom()

Examples

data(Sa_warp)
pks <- get_peaks(Sa_warp, lambda="220")
pk_tab <- get_peaktable(pks)
plot_all_spectra(peak="V13", peak_table = pk_tab, overlapping = TRUE)

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