These methods construct a ggplot object with an annotated plot of a
raw_spct or a raw_mspct object.
# S3 method for raw_spct
autoplot(
object,
...,
w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(),
PhR())),
range = getOption("ggspectra.wlrange", default = NULL),
unit.out = "counts",
pc.out = getOption("ggspectra.pc.out", default = FALSE),
label.qty = "mean",
span = NULL,
wls.target = "HM",
annotations = NULL,
geom = "line",
time.format = "",
tz = "UTC",
norm = "skip",
text.size = 2.5,
idfactor = NULL,
facets = FALSE,
plot.data = "as.is",
ylim = c(NA, NA),
object.label = deparse(substitute(object)),
na.rm = TRUE
)# S3 method for raw_mspct
autoplot(
object,
...,
range = getOption("ggspectra.wlrange", default = NULL),
norm = getOption("ggspectra.norm", default = "skip"),
unit.out = "counts",
pc.out = getOption("ggspectra.pc.out", default = FALSE),
idfactor = TRUE,
facets = FALSE,
plot.data = "as.is",
object.label = deparse(substitute(object)),
na.rm = TRUE
)
A ggplot object with a number of layers that depends on the
data and annotations.
a raw_spct object.
in the case of collections of spectra, additional arguments passed to the plot methods for individual spectra, otherwise currently ignored.
a single waveband object or a list of waveband objects.
an R object on which range() returns a vector of length
2, with minimum and maximum wavelengths (nm).
character IGNORED.
logical, if TRUE use percent instead of fraction of one
for normalized spectral data.
character string giving the type of summary quantity to use
for labels, one of "mean", "total", "contribution",
and "relative".
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.
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.
a character vector. For details please see sections Plot Annotations and Title Annotations.
character The name of a ggplot geometry, currently only
"area", "spct" and "line". The default NULL
selects between them based on stacked.
character Format as accepted by
strptime.
character Time zone to use for title and/or subtitle.
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.
numeric size of text in the plot decorations.
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.
logical or integer Indicating if facets are to be created for
the levels of idfactor when spct contain multiple spectra in
long form.
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.
numeric y axis limits,
character The name of the object being plotted.
logical.
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.
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.
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.
normalize,
raw_spct,
waveband,
photobiologyWavebands-package and
autoplot
Other autoplot methods:
autoplot.calibration_spct(),
autoplot.cps_spct(),
autoplot.filter_spct(),
autoplot.object_spct(),
autoplot.reflector_spct(),
autoplot.response_spct(),
autoplot.source_spct(),
autoplot.waveband(),
set_annotations_default()
low_res.raw_spct <- thin_wl(white_led.raw_spct,
max.wl.step = 20,
max.slope.delta = 0.05,
col.names = "counts_3")
autoplot(low_res.raw_spct)
autoplot(low_res.raw_spct, annotations = "")
two_leds.mspct <-
raw_mspct(list("LED 1" = low_res.raw_spct,
"LED 2" = low_res.raw_spct))
autoplot(two_leds.mspct)
autoplot(two_leds.mspct, facets = 1) # one column
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