plot.peak_table: Plot spectrum from peak table

Description

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

Usage

# S3 method for peak_table
plot(
  x,
  ...,
  loc,
  chrom_list,
  what = "peak",
  chr = "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
)

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). Otherwise, there is no return value.

Arguments

x: The peak table (output from get_peaktable function).
...: Additional arguments.
loc: The name of the peak or retention time that you wish to plot.
chrom_list: A list of chromatograms in matrix form (timepoints x wavelengths).
what: What to look for. Either peak to extract spectral information for a certain peak, rt to scan by retention time, or click to manually select retention time by clicking on the chromatogram. Defaults to peak.
chr: 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 and/or 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.
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, exports spectrum to console. Defaults to FALSE.
verbose: Logical. If TRUE, prints verbose output to console. Defaults to TRUE.

Side effects

If plot_trace is TRUE, plots the chromatographic trace of the specified chromatogram (chr), 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.

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

If box_plot is TRUE, produces a boxplot from the specified peak with groups provided by vars.

Author

Ethan Bass

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.