ggspectra (version 0.3.6)

autoplot.raw_spct: Create a complete ggplot for raw detector-counts spectra.

Description

This function returns a ggplot object with an annotated plot of a raw_spct object.

Usage

# S3 method for raw_spct
autoplot(
  object,
  ...,
  w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(),
    PAR())),
  range = NULL,
  unit.out = "counts",
  pc.out = FALSE,
  label.qty = "mean",
  span = NULL,
  wls.target = "HM",
  annotations = NULL,
  time.format = "",
  tz = "UTC",
  norm = NULL,
  text.size = 2.5,
  idfactor = NULL,
  ylim = c(NA, NA),
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

Arguments

object

a raw_spct object.

...

in the case of collections of spectra, additional arguments passed to the plot methods for individual spectra, otherwise currently ignored.

w.band

a single waveband object or a list of waveband objects.

range

an R object on which range() returns a vector of length 2, with min annd max wavelengths (nm).

unit.out

character IGNORED.

pc.out

logical, if TRUE use percents instead of fraction of one.

label.qty

character string giving the type of summary quantity to use for labels, one of "mean", "total", "contribution", and "relative".

span

a peak is defined as an element in a sequence which is greater than all other elements within a window of width span centered at that element.

wls.target

numeric vector indicating the spectral quantity values for which wavelengths are to be searched and interpolated if need. The character strings "half.maximum" and "half.range" are also accepted as arguments. A list with numeric and/or character values is also accepted.

annotations

a character vector ("summaries" is ignored).

time.format

character Format as accepted by strptime.

tz

character Time zone to use for title and/or subtitle.

norm

numeric normalization wavelength (nm) or character string "max" for normalization at the wavelength of highest peak.

text.size

numeric size of text in the plot decorations.

idfactor

character Name of an index column in data holding a factor with each spectrum in a long-form multispectrum object corresponding to a distinct spectrum. If idfactor=NULL the name of the factor is retrieved from metadata or if no metadata found, the default "spct.idx" is tried.

ylim

numeric y axis limits,

object.label

character The name of the object being plotted.

na.rm

logical.

Value

a ggplot object.

See Also

Other autoplot methods: autoplot.calibration_spct(), autoplot.cps_spct(), autoplot.filter_spct(), autoplot.object_spct(), autoplot.reflector_spct(), autoplot.response_spct(), autoplot.source_spct(), autoplot.waveband(), set_annotations_default()