Create a complete ggplot for a waveband descriptor.

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

Usage

# S3 method for class 'waveband'
autoplot(
  object,
  ...,
  w.length = NULL,
  range = c(280, 800),
  fill = 0,
  span = NULL,
  wls.target = "HM",
  unit.in = getOption("photobiology.radiation.unit", default = "energy"),
  annotations = NULL,
  geom = "line",
  wb.trim = TRUE,
  norm = NULL,
  text.size = 2.5,
  ylim = c(NA, NA),
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

Arguments

object: a waveband object.
...: currently ignored.
w.length: numeric vector of wavelengths (nm)
range: an R object on which range() returns a vector of length 2, with min annd max wavelengths (nm).
fill: value to use as response for wavelngths outside the waveband range.
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.
unit.in: the type of unit we assume as reference "energy" or "photon" based.
annotations: a character vector. For details please see section Plot Annotations.
geom: character The name of a ggplot geometry, currently only "area", "spct" and "line". The default NULL selects between them based on stacked.
wb.trim: logical.
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.
ylim: numeric y axis limits,
object.label: character The name of the object being plotted.
na.rm: logical.

Value

a ggplot object.

Details

Note that scales are expanded so as to make space for the annotations. The object returned is a ggplot object, and can be further manipulated.

Note

Effectiveness spectra are plotted expressing the spectral effectiveness either as \(1 mol^{-1} nm\) photons of \(1 J^{-1} nm\) which can selected through formal argument unit.out. The value of unit.in has no effect on the result when uisng BSWFs, as BSWFs are defined based on a certain base of expression, which is enforced. In contrast, for wavebands which only define a wavelength range, changing the assumed reference irradiance, changes the responsivity according to Plank's law.

This function creates a response_spct object from the waveband object and plots it. Unused arguments are passed along, which means that other plot aspects can be controlled by providing arguments for the plot method of the response_spct class.

Plot Annotations

The recognized annotation names are: "summaries", "peaks", "peak.labels", "valleys", "valley.labels", "wls", "wls.labels", "colour.guide", "color.guide", "boxes", "segments", "labels". In addition, "+" is interpreted as a request to add to the already present default annotations, "-" as request to remove annotations and "=" or missing"+" and "-" as a request to reset annotations to those requested. If used, "+", "-" or "=" must be the first member of a character vector, and followed by one or more of the names given above. To simultaneously add and remove annotations one can pass a list containing character vectors each assembled as described. The vectors are applied in the order they appear in the list. To disable all annotations pass "" or c("=", "") as argument. Adding a variation of an annotation already present, replaces the existing one automatically: e.g., adding "peak.labels" replaces"peaks" if present.

Examples


autoplot(waveband(c(400, 500)))

autoplot(waveband(c(400, 500)), geom = "spct")