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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 .

photon_as_default()
ggplot(sun.spct) +
  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 Bitbucket:

# install.packages("devtools")
devtools::install_bitbucket("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://bitbucket.org/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

© 2015-2020 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

240

Version

0.3.6

License

GPL (>= 2)

Maintainer

Pedro Aphalo

Last Published

April 28th, 2020

Functions in ggspectra (0.3.6)

autoplot.source_spct

Create a complete ggplot for a light-source spectrum.
geom_spct

Spectral data plots.
autoplot.filter_spct

Create a complete ggplot for a filter spectrum.
A_internal_label

Absorbance axis labels
autoplot.object_spct

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

Warn if plot methods is called.
Rfr_specular_label

Reflectance axis labels
A_plot

Create a complete ggplot for a filter spectrum.
R_plot

Create a complete ggplot for a reflector spectrum.
plot.generic_spct

Create a complete ggplot for a spectrum.
autoplot.waveband

Create a complete ggplot for a waveband descriptor.
color_chart

Create a color checker chart
multiplot

Multiple plot function
decoration

Add decorations to spectrum plot (private)
O_plot

Create a complete ggplot for a object spectrum.
GeomSpct

Stat* Objects
autotitle

Add title, subtitle and caption to a spectral plot
scale_y_Tfr_internal_continuous

Transmittance y-scale
scale_y_cps_continuous

Counts-per-second y-scale
cal_plot

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

Create a complete ggplot for an irradiation calibration spectrum.
scale_y_s.e.irrad_continuous

Spectral irradiance y-scale
autoplot.response_spct

Create a complete ggplot for a response spectrum.
scale_y_counts_continuous

Raw-counts y-scale
s.e.response_label

spectral response axis labels
scale_x_wl_continuous

Wavelength x-scale
black_or_white

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

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

Formatter for plain labels discounting for SI multipliers
Tfr_internal_label

Transmittance axis labels
counts_label

Raw-counts axis labels
SI_tg_format

Formatter for tagged labels using SI multipliers
cps_plot

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

Integrate ranges under curve.
scale_y_s.e.response_continuous

Spectral response y-scale
stat_wb_contribution

Integrate ranges under spectral curve.
sec_axis_w_number

Secondary axes for wavelengths
stat_peaks

Find peaks and valleys.
stat_wb_column

Integrate ranges under curve.
w_number

Wavelength conversions
stat_wb_box

Draw colour boxes for wavebands
stat_spikes

Find spikes
stat_wb_mean

Integrate ranges under curve.
autoplot.reflector_spct

Create a complete ggplot for a reflector spectrum.
Afr_plot

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

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

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

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

Absorbance y-scale
exponent2prefix

SI unit prefixes
s.e.irrad_label

spectral irradiance axis labels
w_length_label

Wave- axis labels
ggplot

Create a new ggplot plot from spectral data.
e_plot

Create a complete ggplot for light-source spectra.
decode_annotations

Merge user supplied annotations with default ones
stat_label_peaks

Label peaks and valleys.
cps_label

Counts-per-second axis labels
scale_y_Rfr_specular_continuous

Reflectance y-scale
stat_color

Calculate colours from wavelength.
ggspectra-package

ggspectra: Extensions to 'ggplot2' for Radiation Spectra
stat_wl_summary

Average area under curve for regions.
duration2character

Convert lubridate duration objects to a string if possible
find_idfactor

Find 'idfactor'
stat_wb_label

Label ranges under spectral curve.
e_rsp_plot

Create a complete ggplot for response spectra.
raw_plot

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

Create a complete ggplot for response spectra.
set_annotations_default

Set defaults for autoplot annotations
stat_wb_relative

Integrate ranges under spectral curve.
stat_wb_total

Integrate ranges under spectral curve.
stat_wb_sirrad

Integrate spectral irradiance for wavebands.
subtitle_spct.generic_spct

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

Calculate colours from wavelength.
q_plot

Create a complete ggplot for light-source spectra.
stat_wb_irrad

Integrate irradiance for wavebands.
stat_find_qtys

Find quantity value for target wavelength value.
stat_find_wls

Find wavelength for target quantity value.