autoplot.object_spct: Create a complete ggplot for a object spectrum.

In ggspectra: Extensions to 'ggplot2' for Radiation Spectra

Create a complete ggplot for a object spectrum.

Description

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

Usage

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

## S3 method for class 'object_mspct'
autoplot(
  object,
  ...,
  range = NULL,
  norm = "update",
  plot.qty = getOption("photobiology.filter.qty", default = "all"),
  pc.out = FALSE,
  plot.data = "as.is",
  idfactor = TRUE,
  facets = plot.qty == "all",
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

Arguments

object	an object_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)
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. Always skipped for plot.qty == "all", which is the default.
plot.qty	character string, one of "all", "transmittance", "absorbance", "absorptance", or "reflectance".
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. 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.
stacked	logical Whether to use position_stack() or position_identity().
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 spectrum. If idfactor=NULL the name of the factor is retrieved from metadata or if no metadata found, the default "spct.idx" is tried. If idfactor=NA no aesthetic is mapped to the spectra and the user needs to use 'ggplot2' functions to manually map an aesthetic or use facets for the spectra.
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

The ggplot object returned can be further manipulated and added to. Except when no annotations are added, limits are set for the x-axis and y-axis scales. The y scale limits are expanded to include all data, or at least to the range of expected values. Scales are further expanded so as to make space for the annotations. When all "all" quantities are plotted, a single set of spectra is accepted as input.

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

The method for collections of object spectra of length > 1 is implemented for plot.qty = "all" using facets. Other plot quantities are handled by the methods for filter_spct and reflector_spct objects after on-the-fly conversion.

See Also

normalize, object_spct, waveband, photobiologyWavebands-package and autoplot

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

Examples

low_res.spct <- thin_wl(Ler_leaf.spct,
                        max.wl.step = 20,
                        max.slope.delta = 0.01,
                        col.names = "Tfr")
autoplot(low_res.spct)
autoplot(low_res.spct, geom = "line")

two_leaves.mspct <-
  object_mspct(list("Arabidopsis leaf 1" = low_res.spct,
                    "Arabidopsis leaf 2" = low_res.spct))
autoplot(two_leaves.mspct, idfactor = "Spectra")

ggspectra documentation built on Oct. 22, 2023, 1:07 a.m.