This function returns a ggplot object with an annotated plot from
spectral data contained in a generic_spct
object.
Usage
# S3 method for class 'generic_spct'
autoplot(
object,
...,
y.name,
ymin.name = NULL,
ymax.name = NULL,
ylab = ggplot2::waiver(),
w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(),
PhR())),
range = getOption("ggspectra.wlrange", default = NULL),
norm = NA,
label.qty = "none",
span = NULL,
wls.target = "HM",
annotations = NULL,
time.format = "",
tz = "UTC",
text.size = 2.5,
idfactor = NULL,
facets = FALSE,
ylim = c(NA, NA),
object.label = deparse(substitute(object)),
na.rm = TRUE
)
# S3 method for class 'generic_mspct'
autoplot(object, ...)
Arguments
- object
a generic_spct object.
- ...
in the case of collections of spectra, additional arguments passed to the plot methods for individual spectra, otherwise currently ignored.
- y.name, ymin.name, ymax.name
character Names of the columns to be mapped to the y aesthetic.
- ylab
character or expression The y-axis label.
- 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 No longer supported, normalization is always updated if present and a unit conversion applied.
- 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 withnumeric
and/orcharacter
values is also accepted.- annotations
a character vector. For details please see sections Plot Annotations and Title Annotations.
- 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.
- idfactor
character Name of an index
factor
used to identify each spectrum when multiple spectra are included in a plot. If different from an existing one, renaming takes place. It is used as title for the plot guide and may include embedded spaces and new lines.- facets
logical or integer Indicating if facets are to be created for the levels of
idfactor
whenspct
contain multiple spectra in long form.- ylim
numeric y axis limits,
- object.label
character The name of the object being plotted.
- na.rm
logical.
Details
No automatic plot method is possible for objects of class
generic_spct
as this class is meant to be mainly used only as a pure
base class for derivation. A method is provided for generic_spct
but
not for generic_mspct
as generic_mspct
objects can contain an
assortment of objects including generic_spct
and classes derived
from generic_spct
making the spectra are unlikely be suitable for
plotting in the same ggplot.
Contrary to other autoplot methods, the method for generic_spct
does
not supply defaults to several of its parameters and cannot be used simply
by calling it with the spectrum as argument. There are also limitations on
which annotations are accepted. On-the-fly normalization is not supported.
No method is implemented for generic_mspct
objects as they can
contain an heterogeneous collection of objects of class generic_spct
or any other class derived from it.
Note
If idfactor = NULL
, the default, 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, possibly renaming 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.
See also
normalize
,
generic_spct
,
waveband
,
photobiologyWavebands-package
,
scale_continuous
and
autoplot
Examples
sun.generic_spct <- as.generic_spct(sun.spct)
autoplot(sun.generic_spct, y.name = "s.q.irrad")
autoplot(sun.generic_spct, y.name = "s.e.irrad")
autoplot(sun.generic_spct, y.name = "s.q.irrad",
annotations = "")
autoplot(sun.generic_spct, y.name = "s.q.irrad",
annotations = "title:objt:when",
ylab = s.q.irrad_label(unit.exponent = 0))
autoplot(sun.generic_spct, y.name = "s.e.irrad",
annotations = "colour.guide")
autoplot(sun.generic_spct, y.name = "s.q.irrad",
ylim = c(-1e-6, 4e-6))