ggspectra v0.3.1

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Extensions to 'ggplot2' for Radiation Spectra

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

Readme

ggspectra

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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

This is a basic example which shows plotting using the most automatic approach.

library(photobiology)
library(ggspectra)
plot(sun.spct)

This second example uses the grammar of graphics approach, as implemented in ‘ggplot2’.

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

Type Package
Date 2018-10-28
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 6.1.0
VignetteBuilder knitr
NeedsCompilation no
Packaged 2018-10-29 19:08:39 UTC; aphalo
Repository CRAN
Date/Publication 2018-10-29 20:30:17 UTC

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