Plot one or more

These methods return a ggplot object of an annotated plot from spectral data contained in a filter_spct or a filter_mspct object. Data can be expressed as absorbance, absorptance or transmittance.

Usage

# S3 method for class 'filter_spct'
autoplot(
  object,
  ...,
  w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(),
    PhR())),
  range = getOption("ggspectra.wlrange", default = NULL),
  norm = getOption("ggspectra.norm", default = "update"),
  plot.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  pc.out = getOption("ggspectra.pc.out", default = 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,
  plot.data = "as.is",
  ylim = c(NA, NA),
  object.label = deparse(substitute(object)),
  na.rm = TRUE
)

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

Arguments

object: a filter_spct object or a filter_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 minimum and maximum 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.
plot.qty: character string one of "transmittance" or "absorbance".
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 centred 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.
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.
ylim: numeric y axis limits,
object.label: character The name of the object being plotted.
na.rm: logical.

Value

A ggplot object with a number of layers that depends on the data and annotations.

Details

The plot object returned is a ggplot (an object of class "gg") and it can be added to or modified as any other ggplot. The axis labels are encoded as plotmath expressions as they contain superscripts and special characters. In 'ggplot2', plotmath expressions do not obey theme settings related to text fonts, except for size.

Scale limits are expanded so as to make space for the annotations. If annotations are disabled, limits are not expanded unless reserve.space is passed to parameter annotations.

The generic of the autoplot method is defined in package 'ggplot2'. Package 'ggspectra' defines specializations for the different classes for storage of spectral data defined in package photobiology.

Note

The plotting of absorbance is an exception to scale limits as the y-axis is not extended past 6 a.u. In the case of absorbance, values larger than 6 a.u. are rarely meaningful due to stray light during measurement. However, when transmittance values below the detection limit are rounded to zero, and later converted into absorbance, values Inf a.u. result, disrupting the plot. Scales are further expanded so as to make space for the annotations.

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 multiple spectra is to create a factor named "spct.idx", but if a different name is passed, it will be used instead, possibly renaminig a pre-existing one.

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.

Examples

# one spectrum
autoplot(yellow_gel.spct)

autoplot(yellow_gel.spct, geom = "spct")

autoplot(yellow_gel.spct, plot.qty = "transmittance")

autoplot(yellow_gel.spct, plot.qty = "absorptance")
#> Warning: Conversion from internal Tfr to Afr possible only if Rfr or Rfr.constant are known.

autoplot(yellow_gel.spct, plot.qty = "absorbance")

autoplot(yellow_gel.spct, pc.out = TRUE)

autoplot(yellow_gel.spct, annotations = c("+", "wls"))


# spectra for two filters in long form
autoplot(two_filters.spct)

autoplot(two_filters.spct, idfactor = "Spectra")
#> 'multiple.wl > 1' but no idexing factor found.
#> Warning: Computation failed in `stat_wb_mean()`.
#> Caused by error in `findInterval()`:
#> ! 'vec' must be sorted non-decreasingly and not contain NAs

autoplot(two_filters.spct, facets = TRUE)


# spectra for two filters as a collection
autoplot(two_filters.mspct)

autoplot(two_filters.mspct, idfactor = "Spectra")

autoplot(two_filters.mspct, facets = TRUE)

Plot one or more "filter" spectra.