Create a complete ggplot for a waveband descriptor.
Source:R/autoplot-waveband.R
autoplot.waveband.Rd
This function returns a ggplot object with an annotated plot of a
waveband
object.
Usage
# S3 method for class 'waveband'
autoplot(
object,
...,
w.length = NULL,
range = c(280, 800),
fill = 0,
span = NULL,
wls.target = "HM",
unit.in = getOption("photobiology.radiation.unit", default = "energy"),
annotations = NULL,
geom = "line",
wb.trim = TRUE,
norm = NULL,
text.size = 2.5,
ylim = c(NA, NA),
object.label = deparse(substitute(object)),
na.rm = TRUE
)
Arguments
- object
a waveband object.
- ...
currently ignored.
- w.length
numeric vector of wavelengths (nm)
- range
an R object on which range() returns a vector of length 2, with min annd max wavelengths (nm).
- fill
value to use as response for wavelngths outside the waveband range.
- 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 withnumeric
and/orcharacter
values is also accepted.- unit.in
the type of unit we assume as reference "energy" or "photon" based.
- annotations
a character vector. For details please see section Plot Annotations.
- geom
character The name of a ggplot geometry, currently only
"area"
,"spct"
and"line"
. The defaultNULL
selects between them based onstacked
.- wb.trim
logical.
- norm
numeric normalization wavelength (nm) or character string "max" for normalization at the wavelength of highest peak.
- text.size
numeric size of text in the plot decorations.
- ylim
numeric y axis limits,
- object.label
character The name of the object being plotted.
- na.rm
logical.
Details
Note that scales are expanded so as to make space for the annotations. The object returned is a ggplot object, and can be further manipulated.
Note
Effectiveness spectra are plotted expressing the spectral effectiveness
either as \(1 mol^{-1} nm\) photons of \(1 J^{-1} nm\) which can selected through
formal argument unit.out
. The value of unit.in
has no effect on
the result when uisng BSWFs, as BSWFs are defined based on a certain base of
expression, which is enforced. In contrast, for wavebands which only define a
wavelength range, changing the assumed reference irradiance, changes the
responsivity according to Plank's law.
This function creates a response_spct
object from the waveband
object and plots it. Unused arguments are passed along, which means that
other plot aspects can be controlled by providing arguments for the plot
method of the response_spct
class.
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.
See also
autoplot.response_spct
,
waveband
.
Other autoplot methods:
autoplot.calibration_spct()
,
autoplot.cps_spct()
,
autoplot.filter_spct()
,
autoplot.object_spct()
,
autoplot.raw_spct()
,
autoplot.reflector_spct()
,
autoplot.response_spct()
,
autoplot.source_spct()
,
set_annotations_default()