Package `ggspectra` provides a set of layer functions and
autoplot() methods extending packages `ggplot2` and `photobiology`.
The autoplot() methods specialised for objects of classes defined in
package 'photobiology' facilitate in many respects the plotting of spectral
data. The ggplot() methods specialised for objects of classes
defined in package 'photobiology' combined with the new layer functions and
scales easy the task of flexibly plotting radiation-related spectra and of
annotating the resulting plots.
These methods, layer functions and scales are
specialized and work only with certain types of data and ways of expressing
physical quantities. Most importantly, all statistics expect the
values mapped to the x aesthetic to be wavelengths expressed in
nanometres (nm), which is ensured when the data are stored in data objects
of classes defined in package 'photobiology'. The support for scale transforms
is manual and only partial. Flipping is not supported.
Although originally aimed at plots relevant to photobiology, many
of the functions in the package are also useful for plotting other UV, VIS
and NIR spectra of light emission, transmittance, reflectance, absorptance,
and responses.
The available summary quantities are both simple statistical summaries and
response-weighted summaries. Simple derived quantities represent summaries of a
given range of wavelengths, and can be expressed either in energy or photon
based units. Derived biologically effective quantities are used to quantify
the effect of radiation on different organisms or processes within organisms.
These effects can range from damage to perception of informational light
signals. Additional features of spectra may be important and worthwhile
annotating in plots. Of these, local maxima (peaks), minima (valleys) and spikes
present in spectral data can also be annotated with statistics from 'ggspectra'.
Package 'ggspectra' is useful solely for plotting spectral data as most
functions depend on the x aesthetic being mapped to a variable containing
wavelength values expressed in nanometres. It works well together with
many other extensions to package 'ggplot2' such as packages 'ggrepel',
'gganimate' and 'cowplot'.
This package is part of a suite of R packages for photobiological
calculations described at the
[r4photobiology](https://www.r4photobiology.info) web site.
