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Plot all spectra for chosen peak

Source: R/plot_spectrum.R
plot_all_spectra.Rd

Plot the spectra of a peak from several chromatograms. Wrapper for plot_spectrum.

Usage

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

Arguments

loc

The peak, retention time, or scan index from which to extract spectral data.

peak_table

A peak_table object created by get_peaktable.

chrom_list

A list of chromatograms in matrix format (timepoints × wavelengths). If no argument is provided here, the function will try to find the chrom_list object using the pointer in the peak_table.

idx

Vector of chromatograms to plot, or "all" (the default).

engine

Plotting backend to use. One of "base", "ggplot", or "plotly". "ggplot2" is also accepted here, for backward compatibility, but "ggplot" is the spelling the other plotting functions take.

plot_spectrum

Logical. If TRUE, plots the spectrum of the chosen peak. Defaults to TRUE.

export_spectrum

Logical. If TRUE (the default), invisibly returns the spectra as a data.frame.

scale_spectrum

Logical. If TRUE (the default), scales each spectrum to the range [0, 1].

overlapping

Logical. If TRUE (the default), plots the spectra on a single plot. Used only when engine = "base".

verbose

Logical. If TRUE, prints the index and name of each chromatogram plotted, with its retention time, wavelength and absorbance. Defaults to FALSE.

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.

peak

The peak argument is deprecated. Please use loc instead.

...

Additional arguments to plot_spectrum.

Value

  • If export_spectrum = TRUE (the default), invisibly returns a data.frame with wavelengths as rows and one column per sample encoding absorbance at each wavelength (normalized if scale_spectrum = TRUE).

  • If export_spectrum = FALSE, returns a plotly or ggplot object, or nothing if engine == "base".

Side effects

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

See also

Other visualization functions: boxplot.peak_table(), mirror_plot(), plot.chrom_list(), plot.matched_peak_list(), plot.peak_list(), plot.peak_table(), plot_chrom_contour(), plot_chroms(), plot_chroms_heatmap(), plot_spectrum(), scan_chrom()

Author

Ethan Bass

Examples

data(Sa_warp)
pks <- get_peaks(Sa_warp, lambda = "220")
pk_tab <- get_peaktable(pks)
plot_all_spectra(loc = "V11", peak_table = pk_tab, overlapping = TRUE)