View source: R/autoplot-generic-spct.R
autoplot.generic_spct | R Documentation |
This function returns a ggplot object with an annotated plot of a generic_spct object.
## 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 = NULL,
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, ...)
object |
a cps_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 min annd max wavelengths (nm). |
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 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
|
annotations |
a character vector ("summaries" is ignored). For details please see sections Plot Annotations and Title Annotations. |
time.format |
character Format as accepted by |
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 column in data holding a
|
facets |
logical or integer Indicating if facets are to be created for
the levels of |
ylim |
numeric y axis limits (expansion only!). |
object.label |
character The name of the object being plotted. |
na.rm |
logical. |
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.
a ggplot
object.
A ggplot
object.
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.
Scales are expanded so as to make space for the annotations if these are present. The object returned is a ggplot object, and can be further manipulated.
normalize
,
generic_spct
,
waveband
,
photobiologyWavebands-package
,
scale_continuous
and
autoplot
sun.generic_spct <- as.generic_spct(sun.spct)
autoplot(sun.generic_spct, y.name = "s.q.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))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.