ggspectra v0.3.2

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Extensions to 'ggplot2' for Radiation Spectra

Additional annotations, stats, geoms and scales for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and autoplot() methods for spectral data and waveband definitions stored in objects of classes defined in package 'photobiology'. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Readme

ggspectra

cran version cran checks

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.

Example

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 (http://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 (http://hdl.handle.net/10138/37558).

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

© 2015-2018 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.

Functions in ggspectra

Name Description
autoplot.cps_spct Create a complete ggplot for detector-counts per second spectra.
black_or_white Chose black vs. white color based on weighted mean of RGB channels
q_plot Create a complete ggplot for light-source spectra.
cal_plot Create a complete ggplot for an irradiation calibration spectrum.
q_rsp_plot Create a complete ggplot for response spectra.
scale_y_cps_continuous Counts-per-second y-scale
scale_y_s.e.irrad_continuous Spectral irradiance y-scale
autoplot.filter_spct Create a complete ggplot for a filter spectrum.
autoplot.generic_spct Warn if plot methods is called.
Afr_plot Create a complete ggplot for a filter spectrum.
SI_pl_format Formatter for plain labels discounting for SI multipliers
R_plot Create a complete ggplot for a reflector spectrum.
SI_tg_format Formatter for tagged labels using SI multipliers
Rfr_specular_label Reflectance axis labels
O_plot Create a complete ggplot for a object spectrum.
autoplot.object_spct Create a complete ggplot for a object spectrum.
cps_label Counts-per-second axis labels
cps_plot Create a complete ggplot for detector-counts per second spectra.
autoplot.raw_spct Create a complete ggplot for raw detector-counts spectra.
GeomSpct Stat* Objects
find_idfactor Find 'idfactor'
autoplot.reflector_spct Create a complete ggplot for a reflector spectrum.
autoplot.response_spct Create a complete ggplot for a response spectrum.
ggplot Create a new ggplot plot from spectral data.
geom_spct Spectral data plots.
decode_annotations Merge user supplied annotations with default ones
scale_y_Tfr_internal_continuous Transmittance y-scale
decoration Add decorations to spectrum plot (private)
color_chart Create a color checker chart
scale_y_counts_continuous Raw-counts y-scale
counts_label Raw-counts axis labels
e_rsp_plot Create a complete ggplot for response spectra.
multiplot Multiple plot function
exponent2prefix SI unit prefixes
plot.generic_spct Create a complete ggplot for a spectrum.
raw_plot Create a complete ggplot for raw detector-counts spectra.
s.e.irrad_label spectral irradiance axis labels
s.e.response_label spectral response axis labels
sec_axis_w_number Secondary axes for wavelengths
scale_y_s.e.response_continuous Spectral response y-scale
stat_find_wls Find wavelength for target quantity value.
T_plot Create a complete ggplot for a filter spectrum.
scale_y_A_internal_continuous Absorbance y-scale
scale_x_wl_continuous Wavelength x-scale
stat_peaks Find peaks and valleys.
scale_y_Rfr_specular_continuous Reflectance y-scale
stat_wb_hbar Integrate ranges under curve.
stat_label_peaks Label peaks and valleys.
stat_wb_total Integrate ranges under spectral curve.
stat_wb_box Draw colour boxes for wavebands
Tfr_internal_label Transmittance axis labels
stat_wb_irrad Integrate irradiance for wavebands.
stat_wb_label Label ranges under spectral curve.
autoplot.source_spct Create a complete ggplot for a light-source spectrum.
stat_wb_relative Integrate ranges under spectral curve.
autoplot.waveband Create a complete ggplot for a waveband descriptor.
stat_wb_sirrad Integrate spectral irradiance for wavebands.
title_spct Build a plot title from object metadata (deprecated!)
stat_wb_mean Integrate ranges under curve.
w_length_label Wave- axis labels
stat_wl_strip Calculate colours from wavelength.
w_number Wavelength conversions
duration2character Convert lubridate duration objects to a string if possible
e_plot Create a complete ggplot for light-source spectra.
ggspectra-package ggspectra: Extensions to 'ggplot2' for Radiation Spectra
ggtitle_spct Add title to a spectral plot
stat_color Calculate colours from wavelength.
stat_find_qtys Find quantity value for target wavelength value.
stat_wb_column Integrate ranges under curve.
stat_wb_contribution Integrate ranges under spectral curve.
stat_wl_summary Average area under curve for regions.
subtitle_spct.generic_spct Build a plot subtitle from object metadata (deprecated!)
A_internal_label Absorbance axis labels
A_plot Create a complete ggplot for a filter spectrum.
autoplot.calibration_spct Create a complete ggplot for an irradiation calibration spectrum.
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Vignettes of ggspectra

Name
userguide1-grammar.Rmd
userguide2-autoplot-methods.Rmd
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Details

Type Package
Date 2019-02-19
License GPL (>= 2)
LazyData TRUE
LazyLoad TRUE
ByteCompile TRUE
URL https://www.r4photobiology.info, https://bitbucket.org/aphalo/ggspectra
BugReports https://bitbucket.org/aphalo/ggspectra
Encoding UTF-8
RoxygenNote 6.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2019-02-20 11:51:42 UTC; aphalo
Repository CRAN
Date/Publication 2019-02-20 13:20:03 UTC

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