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ggspectra

The goal of ‘ggspectra’ is to make it easy to plot radiation spectra and similar data, such and transmittance, absorbance and reflectance spectra, producing fully annotated publication- and presentation-ready plots. It is an extension to packages ‘ggplot2’ and ‘photobiology’, and part of the ‘r4phototbiology’ suite.

Package ‘ggspectra’ provides stats, geoms, scales and functions to be used for plotting radiation-related spectra and annotating the plots with quantities derived from spectral data. All summary quantities implemented in ‘photobiology’ can be used for annotations including biologically effective irradiances and exposures.

Please, see the web site r4photobiology for details on other packages available as part of the suite, and on how to install them.

Examples

Plotting spectra with an specialization of the autoplot() method provides the most automatic approach.

library(ggspectra)
autoplot(sun.spct)

Some degree of flexibility can be obtained by passing arguments.

autoplot(sun.spct, annotations = c("+", "title:where:when"), unit.out = "photon")

Maximum flexibilty is achieved when building a plot layer by layer using the grammar of graphics approach, as implemented in ‘ggplot2’, but taking advantage of the specialized ggplot() methods, geometries, statistics and scales specialized for the plotting of spectra, defined in this package .

ggplot(sun.spct, unit.out = "photon") +
  geom_spct() +
  scale_y_s.q.irrad_continuous() +
  scale_x_wl_continuous(sec.axis = sec_axis_w_number()) +
  theme_bw()

Installation

Installation of the most recent stable version from CRAN:

install.packages("ggspectra")

Installation of the current unstable version from GitHub:

# install.packages("remotes")
remotes::install_github("aphalo/ggspectra")

Documentation

HTML documentation is available at (https://docs.r4photobiology.info/ggspectra/), including a User Guide.

News on updates to the different packages of the ‘r4photobiology’ suite are regularly posted at (https://www.r4photobiology.info/).

Two articles introduce the basic ideas behind the design of the suite and its use: Aphalo P. J. (2015) (https://doi.org/10.19232/uv4pb.2015.1.14) and Aphalo P. J. (2016) (https://doi.org/10.19232/uv4pb.2016.1.15).

A book is under preparation, and the draft is currently available at (https://leanpub.com/r4photobiology/). The book conatins many examples of plots created with ‘ggspectra’.

A handbook written before the suite was developed contains useful information on the quantification and manipulation of ultraviolet and visible radiation: Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., & Rosenqvist, E. (Eds.) (2012) Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). PDF file available from (https://doi.org/10.31885/9789521083631).

Contributing

Pull requests, bug reports, and feature requests are welcome at (https://github.com/aphalo/ggspectra).

Citation

If you use this package to produce scientific or commercial publications, please cite according to:

citation("ggspectra")
#> 
#> To cite package 'ggspectra' in publications, please use:
#> 
#>   Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin,
#>   2015:1, 21-29. DOI:10.19232/uv4pb.2015.1.14
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     author = {Pedro J. Aphalo},
#>     title = {The r4photobiology suite},
#>     journal = {UV4Plants Bulletin},
#>     volume = {2015},
#>     number = {1},
#>     pages = {21-29},
#>     year = {2015},
#>     doi = {10.19232/uv4pb.2015.1.14},
#>   }

License

© 2015-2023 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.

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Version

Install

install.packages('ggspectra')

Monthly Downloads

594

Version

0.3.12

License

GPL (>= 2)

Issues

7

Pull Requests

0

Stars

5

Forks

0

Maintainer

Pedro Aphalo

Last Published

October 21st, 2023

Functions in ggspectra (0.3.12)

Tfr_label

Transmittance axis labels
autoplot.response_spct

Create a complete ggplot for a response spectrum.
autoplot.calibration_spct

Create a complete ggplot for an irradiation calibration spectrum.
autoplot.source_spct

Create a complete ggplot for light-source spectra.
autoplot.generic_spct

Create a complete ggplot for generic spectral data.
autoplot.object_spct

Create a complete ggplot for a object spectrum.
autoplot.cps_spct

Create a complete ggplot for detector-counts per second spectra.
autoplot.raw_spct

Create a complete ggplot for raw detector-counts spectra.
autoplot.filter_spct

Create a complete ggplot for a filter spectrum.
autoplot.reflector_spct

Create a complete ggplot for a reflector spectrum.
cps_label

Counts-per-second axis labels
counts_label

Raw-counts axis labels
cal_plot

Create a complete ggplot for an irradiation calibration spectrum.
color_chart

Create a color checker chart
autoplot.waveband

Create a complete ggplot for a waveband descriptor.
autotitle

Add title, subtitle and caption to a spectral plot
exponent2prefix

SI unit prefixes
ggplot

Create a new ggplot plot from spectral data.
find_idfactor

Find 'idfactor'
decode_annotations

Merge user supplied annotations with default ones
cps_plot

Create a complete ggplot for detector-counts per second spectra.
GeomSpct

Stat* Objects
e_rsp_plot

Create a complete ggplot for response spectra.
e_plot

Create a complete ggplot for light-source spectra.
duration2character

Convert lubridate duration objects to a string if possible
decoration

Add decorations to spectrum plot (private)
multiplot

Multiple plot function
scale_y_Tfr_continuous

Transmittance y-scale
q_plot

Create a complete ggplot for light-source spectra.
multipliers_label

Calibration multipliers axis labels
ggspectra-package

ggspectra: Extensions to 'ggplot2' for Radiation Spectra
black_or_white

Chose black vs. white color based on weighted mean of RGB channels
axis_labels

Default text for axis labels
scale_x_wavenumber_continuous

Wavenumber x-scale
q_rsp_plot

Create a complete ggplot for response spectra.
scale_x_frequency_continuous

Frequency x-scale
plot.generic_spct

Deprecated plot methods
scale_y_Rfr_continuous

Reflectance y-scale
sec_axis_w_number

Secondary axes for wavelengths
set_annotations_default

Set defaults for autoplot annotations
scale_y_Afr_continuous

Absorptance y-scale
generic_plot

Create a complete ggplot for generic spectral data.
s.e.irrad_label

spectral irradiance axis labels
geom_spct

Spectral data plots.
raw_plot

Create a complete ggplot for raw detector-counts spectra.
stat_color

Calculate colours from wavelength.
stat_find_qtys

Find quantity value for target wavelength value.
scale_y_counts_continuous

Raw-counts y-scale
s.e.response_label

spectral response and action axis labels
scale_y_cps_continuous

Counts-per-second y-scale
scale_x_energy_eV_continuous

Energy per photon x-scale
stat_wb_irrad

Integrate irradiance for wavebands.
stat_peaks

Find peaks and valleys.
stat_spikes

Find spikes
validate_idfactor

Validate idfactor
stat_wb_label

Label ranges under spectral curve.
subtitle_spct.generic_spct

Build a plot subtitle from object metadata (deprecated!)
title_spct

Build a plot title from object metadata (deprecated!)
stat_wb_column

Integrate ranges under curve.
stat_wb_box

Draw colour boxes for wavebands
stat_label_peaks

Label peaks and valleys.
stat_find_wls

Find wavelength for target quantity value.
stat_wb_total

Integrate ranges under spectral curve.
stat_wl_strip

Calculate colours from wavelength.
stat_wb_sirrad

Integrate spectral irradiance for wavebands.
scale_y_multipliers_continuous

Calibration multipliers y-scale
stat_wl_summary

Average area under curve for regions.
scale_y_s.e.response_continuous

Spectral response and action y-scales
scale_y_s.e.irrad_continuous

Spectral irradiance y-scale
w_length_label

Wave- axis labels
scale_x_wl_continuous

Wavelength x-scale
scale_y_A_continuous

Absorbance y-scale
stat_wb_relative

Integrate ranges under spectral curve.
stat_wb_mean

Integrate ranges under curve.
stat_wb_contribution

Integrate ranges under spectral curve.
w_number

Deprecated functions
stat_wb_hbar

Integrate ranges under curve.
A_label

Absorbance axis labels
O_plot

Create a complete ggplot for a object spectrum.
Afr_label

Absorptance axis labels
SI_pl_format

Formatter for plain labels discounting for SI multipliers
Rfr_label

Reflectance axis labels
A_plot

Create a complete ggplot for a filter spectrum.
Afr_plot

Create a complete ggplot for a filter spectrum.
T_plot

Create a complete ggplot for a filter spectrum.
R_plot

Create a complete ggplot for a reflector spectrum.
SI_tg_format

Formatter for tagged labels using SI multipliers