Plot spectrum from peak table

Plots the trace and/or spectrum for a given peak in peak table.

Usage

# S3 method for class 'peak_table'
plot(
  x,
  loc,
  chrom_list = NULL,
  what = "peak",
  idx = "max",
  lambda = "max",
  plot_spectrum = TRUE,
  plot_trace = TRUE,
  box_plot = FALSE,
  vars = NULL,
  spectrum_labels = TRUE,
  scale_spectrum = FALSE,
  export_spectrum = FALSE,
  verbose = TRUE,
  engine = c("base", "plotly", "ggplot"),
  ...
)

Arguments

x: The peak table (output from get_peaktable).
loc: A vector specifying the peak(s) or retention time(s) to plot.
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 using the pointer in the peak_table.
what: What to look for. Either peak to extract spectral information for a certain peak, rt to scan by retention time, idx to scan by numeric index, or click to manually select retention time by clicking on the chromatogram. Defaults to "peak" mode.
idx: Numerical index of chromatogram you wish to plot; "max" to plot the chromatogram with the largest signal; or "all" to plot spectra for all chromatograms.
lambda: The wavelength you wish to plot the trace at (if plot_chrom is TRUE. Otherwise, the wavelength to be used for the determination of signal abundance.
plot_spectrum: Logical. If TRUE, plots the spectrum of the chosen peak. Defaults to TRUE.
plot_trace: Logical. If TRUE, plots the trace of the chosen peak at lambda. Defaults to TRUE.
box_plot: Logical. If TRUE, plots box plot using categories defined by vars.
vars: Independent variables for boxplot. Righthand side of formula.
spectrum_labels: Logical. If TRUE, plots labels on maxima in spectral plot. Defaults to TRUE.
scale_spectrum: Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.
export_spectrum: Logical. If TRUE, invisibly returns the spectrum as a data.frame. Defaults to FALSE.
verbose: Logical. If TRUE (default), prints verbose output to the console.
engine: Which plotting engine to use: base, ggplot2, or plotly.
...: Additional arguments to boxplot.

Value

If export_spectrum = FALSE (default), a plotly or ggplot object, or nothing if engine == "base".
If export_spectrum = TRUE, invisibly returns the spectrum as a data.frame with wavelengths as rows and a single column per sample encoding absorbance at each wavelength (normalized if scale_spectrum = TRUE). Otherwise, if engine == "base", there is no return value. If export_spectrum is TRUE, returns the spectrum as a data.frame with wavelengths as rows and columns encoding the absorbance (or normalized absorbance, if scale_spectrum is TRUE) for the specified sample(s).

Details

Can be used to confirm the identity of a peak or check that a particular column in the peak table represents a single compound. Can also be used to create simple box-plots to examine the distribution of a peak with respect to variables defined in sample metadata.

When plot_trace is TRUE, plots the chromatographic trace of the specified chromatogram (idx), at the specified wavelength (lambda) with a dotted red line to indicate the retention time given by loc. The trace is a single column from the chromatographic matrix. When plot_spectrum is TRUE, plots the spectrum for the specified chromatogram at the specified retention time. The spectrum represents a single row from the chromatographic matrix. When box_plot is TRUE, produces a boxplot from the specified peak with groups defined by the vars argument.

Side effects

If engine == "base", plots are rendered to the active graphics device.

Author

Ethan Bass