visualisation-methods-spectra: Visualisation methods

In GaelleLefort/ASICS: Automatic Statistical Identification in Complex Spectra

Description

Methods available to plot one object in ASICS package.

Usage

## S4 method for signature 'Spectra,ANY'
plot(x, y, xlim = c(0.5, 10), ylim = NULL, ...)

## S4 method for signature 'ASICSResults,ANY'
plot(
  x,
  y,
  idx = 1,
  xlim = c(0.5, 10),
  ylim = NULL,
  pure.library = NULL,
  add.metab = NULL,
  ...
)

Arguments

x	An object of class Spectra, PureLibrary or ASICSResults.
y	Currently not used.
xlim, ylim	Boundaries for x and y, respectively.
...	Currently not used.
idx	Index of the spectrum to plot. Default to 1.
pure.library	Pure library used for the quantification. Default to NULL (in which case, the library included in the package is used).
add.metab	Name of one metabolite to add to the plot. Default to NULL (in which case, no pure spectrum added to the plot).

Value

• A ggplot plot of all spectra (or of a subset) on the same figure for Spectra and PureLibrary objects.

• A ggplot plot of original and reconstructed spectra of one sample in the same figure for ASICSResults object. In addition, one pure metabolite spectrum (as provided in the reference library) and the deformed one can be superimposed to the plot.

Examples

# Import data and create object
current_path <- system.file("extdata", "example_spectra", package = "ASICS")
spectra_data <- importSpectraBruker(current_path)
spectra_obj <- createSpectra(spectra_data)
spectra_obj <- createSpectra(spectra_data)

# Plot the spectra
plot(spectra_obj)

GaelleLefort/ASICS documentation built on July 19, 2020, 2:08 p.m.