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Plot spectrum from peak table

Source: R/plot.peak_table.R
plot.peak_table.Rd

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",
  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"),
  chr = NULL,
  ...
)

Arguments

x

The peak table (output from get_peaktable function).

loc

A vector specifying the peak(s) or retention time(s) that you wish 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 used to create the peak_table.

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.

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 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. 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, exports spectrum to console. Defaults to FALSE.

verbose

Logical. If TRUE, prints verbose output to console. Defaults to TRUE.

engine

Which plotting engine to use: either base or plotly.

chr

Deprecated. Please use idx instead.

...

Additional arguments to boxplot.

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.

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.

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