Set R options controlling default arguments for some formal parameters in methods and functions from package 'ggspectra'.
set_annotations_default(annotations = NULL)set_w.band_default(w.band = NULL)
set_markup_format_default(markup.format = NULL)
set_plot_range_default(range = NULL)
set_pc_out_default(pc.out = TRUE)
set_axis_symbols_default(axis.symbols = TRUE)
Previous value of the option, returned invisibly. This is a named
list of length one as returned by options, that can be passed
unchanged as argument to R function options or in a new call to the
same function that returned it.
a character vector. For details please see sections Plot Annotations and Title Annotations.
a single waveband object or a list of waveband objects.
character string, "R", "R.expression", "r.character", or "LaTeX".
an R object on which range() returns a vector of length
2, with minimum and maximum wavelengths (nm).
logical, if TRUE use percent instead of fraction of one
for normalized spectral data.
logical If TRUE symbols of the quantities are
added to the default name.
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.
The annotation layers are added to the plot using statistics defined in 'ggspectra':
stat_peaks, stat_valleys,
stat_label_peaks, stat_label_valleys,
stat_find_wls, stat_spikes,
stat_wb_total, stat_wb_mean,
stat_wb_irrad, stat_wb_sirrad,
stat_wb_contribution, stat_wb_relative,
and stat_wl_strip. However, only some of their parameters
can be passed arguments through autoplot methods. In some cases
the defaults used by autoplot methods are not the defaults of the
statistics.
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 values accepted, syntax used and behaviour are the same as when passing
arguments to formal parameters in function and methods calls, except that
NULL as argument clears the R option. To restore the previous state
of an option, save the value returned and pass it as argument in a later
call to the same function.
Changing the defaults with options, instead of affecting a single function
call (e.g., affecting a single plot or layer in a plot), changes the default
used for all subsequent function calls calls when when no argument is passed
explicitly. This makes it possible to easily change in one place in a script
the appearance of all/multiple plots. Using these functions functions instead
of options to set the defaults adds a validation step that
protects from errors triggered in subsequent function calls.
R option photobiology.plot.annotations controls the default for formal
parameter annotations in autoplot methods and in
function decoration.
R option photobiology.plot.bands controls the default for formal
parameter w.band in autoplot methods and in
function decoration.
R option photobiology.math controls the default for
formal parameter markup.format or format in
different axis label and scale functions.
R option ggspectra.wlrange controls the default for
formal parameter range in autoplot methods.
R option ggspectra.pc.out controls the default for
formal parameter pc.out in autoplot methods that
have this formal parameter.
R option ggspectra.axis.symbols controls the default for
formal parameter axis.symbols in
different axis label and scale functions.
Additional argument defaults are controlled by options also used in
package 'photobiology'. See energy_as_default,
using_Tfr and options.