autoplot.filter_spct {ggspectra}

Create a complete ggplot for a filter spectrum.

Description

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

Usage

## S3 method for class 'filter_spct'
autoplot(
  object,
  ...,
  w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(),
    PhR())),
  range = NULL,
  norm = getOption("ggspectra.norm", default = "update"),
  plot.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  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 'filter_mspct'
autoplot(
  object,
  ...,
  range = NULL,
  norm = getOption("ggspectra.norm", default = "update"),
  plot.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  pc.out = 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 autoplot 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 and 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.

plot.qty

character string one of "transmittance" or "absorbance".

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 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 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. The plotting of absorbance is an exception 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.

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.

See Also

normalize, filter_spct, waveband, photobiologyWavebands-package and autoplot

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

Examples

autoplot(yellow_gel.spct)
autoplot(yellow_gel.spct, geom = "spct")
autoplot(yellow_gel.spct, plot.qty = "transmittance")
autoplot(yellow_gel.spct, plot.qty = "absorptance")
autoplot(yellow_gel.spct, plot.qty = "absorbance")
autoplot(yellow_gel.spct, pc.out = TRUE)
autoplot(yellow_gel.spct, annotations = c("+", "wls"))

two_filters.mspct <-
 filter_mspct(list("Yellow gel" = yellow_gel.spct,
                   "Polyester film" = polyester.spct))
autoplot(two_filters.mspct)
autoplot(two_filters.mspct, idfactor = "Spectra")
autoplot(two_filters.mspct, facets = TRUE)