photobiology (version 0.11.3)

setNormalized: Set the "normalized" and "normalization" attributes

Description

Function to write the "normalized" attribute of an existing generic_spct object.

Usage

setNormalized(
  x,
  norm = FALSE,
  norm.type = NA_character_,
  norm.factors = NA_real_,
  norm.cols = NA_character_,
  norm.range = rep(NA_real_, 2),
  verbose = getOption("verbose_as_default", default = FALSE)
)
setNormalised(
  x,
  norm = FALSE,
  norm.type = NA_character_,
  norm.factors = NA_real_,
  norm.cols = NA_character_,
  norm.range = rep(NA_real_, 2),
  verbose = getOption("verbose_as_default", default = FALSE)
)

Arguments

x

a generic_spct object.

norm

numeric (or logical) Normalization wavelength (nanometres).

norm.type

character Type of normalization applied.

norm.factors

numeric The scaling factor(s) so that dividing the spectral values by this factor reverts the normalization.

norm.cols

character The name(s) of the data columns normalized.

norm.range

numeric The wavelength range used for normalization (nm).

verbose

logical Flag enabling or silencing informative warnings.

Details

This function is used internally, although occasionally users may want to use it to "pretend" that spectral data have not been normalized. Use normalize() methods to apply a normalization and set the attributes accordingly. Function setNormalized() only sets the attributes that store the metadata corresponding to an already applied normalization. Thus a trace of the transformations applied to spectral data is kept, which currently is used to renormalize the spectra when the quantity used for expression is changed with a conversion function. It is also used in other packages like 'ggspectra' when generating automatically axis labels. If x is not a generic_spct object, x is not modified.

See Also

Other rescaling functions: fscale(), fshift(), getNormalized(), getScaled(), is_normalized(), is_scaled(), normalize(), setScaled()