autoplot.source_spct {ggspectra}

Create a complete ggplot for light-source spectra.

Description

These methods return a ggplot object with an annotated plot of a source_spct object or of the spectra contained in a source_mspct object.

Usage

## S3 method for class 'source_spct'
autoplot(
  object,
  ...,
  w.band = getOption("photobiology.plot.bands", default =
    list(photobiologyWavebands::UVC(), photobiologyWavebands::UVB(),
    photobiologyWavebands::UVA(), photobiologyWavebands::PhR())),
  range = NULL,
  norm = getOption("ggspectra.norm", default = "update"),
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  pc.out = FALSE,
  label.qty = NULL,
  span = NULL,
  wls.target = "HM",
  annotations = NULL,
  geom = "line",
  time.format = "",
  tz = "UTC",
  text.size = 2.5,
  chroma.type = "CMF",
  idfactor = NULL,
  facets = FALSE,
  ylim = c(NA, NA),
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

## S3 method for class 'source_mspct'
autoplot(
  object,
  ...,
  range = NULL,
  norm = getOption("ggspectra.normalize", default = "update"),
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  pc.out = FALSE,
  idfactor = TRUE,
  facets = FALSE,
  plot.data = "as.is",
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

Arguments

object

a source_spct or a source_mspct 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).

norm

numeric Normalization wavelength (nm) or character string "max", or "min" for normalization at the corresponding wavelength, "update" to update the normalization after modifying units of expression, quantity or range but respecting the previously used criterion, or "skip" to force return of object unchanged.

unit.out

character string indicating type of radiation units to use for plotting: "photon" or its synonym "quantum", or "energy".

pc.out

logical, if TRUE use percent instead of fraction of one for normalized spectral data.

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. For details please see sections Plot Annotations and Title Annotations.

geom

character The name of a ggplot geometry, currently only "area", "spct" and "line". The default NULL selects between them based on stacked.

time.format

character Format as accepted by strptime.

tz

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

text.size

numeric size of text in the plot decorations.

chroma.type

character one of "CMF" (color matching function) or "CC" (color coordinates) or a chroma_spct object.

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 level of the factor.

facets

logical or integer Indicating if facets are to be created for the levels of idfactor when spct contain multiple spectra in long form.

ylim

numeric y axis limits,

object.label

character The name of the object being plotted.

na.rm

logical.

plot.data

character Data to plot. Default is "as.is" plotting one line per spectrum. When passing "mean", "median", "sum", "prod", var", "sd", "se" as argument all the spectra must contain data at the same wavelength values.

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 and added to.

Value

a ggplot object.

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.

Title Annotations

metadata retrieved from object object is paased to ggplot2::ggtitle() as arguments for title, subtitle and caption. The specification for the title is passed as argument to annotations, and consists in the keyword title with optional modifiers selecting the kind of metatdata to use, separated by colons. Up to three keywords separated by colons are accepted, and correspond to title, subtitle and caption. The recognized keywords are: "objt", "class", "what", "when", "where", "how", "inst.name", "inst.sn", "comment" and "none" are recognized as modifiers to "title"; "none" is a placeholder. Default is "title:objt" or no title depending on the context.

Note

If idfactor = NULL, the default for single spectra, the name of the factor is retrieved from metadata or if no metadata found, the default "spct.idx" is tried. The default for collections of spectra is to create a factor named "spct.idx", but if a different name is passed, it will be used instead.

See Also

normalize, source_spct, waveband, photobiologyWavebands-package and autoplot

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

Examples

autoplot(sun.spct)
autoplot(sun.spct, geom = "spct")
autoplot(sun.spct, unit.out = "photon")
autoplot(sun.spct, norm = "max")

two_suns.mspct <- source_mspct(list(sun1 = sun.spct, sun2 = sun.spct / 2))
autoplot(two_suns.mspct)
autoplot(two_suns.mspct, facets = 1) # one column
autoplot(two_suns.mspct, facets = 2) # two columns
autoplot(two_suns.mspct, plot.data = "mean")