Changelog • ggspectra

ggspectra 0.3.15

Fix a bug in autotitle() affecting only collections of spectra where all spectra have the same value for the when.measured attribute and this attribute is used in title annotations.

ggspectra 0.3.14

CRAN release: 2024-11-13

Ensure compatibility with upcoming ‘ggplot2’ 3.5.2: Use geom_linerange() instead of geom_errorbarh() as default in stat_wb_hbar().
Make the order of parameters of layer functions consistent with those in ‘ggplot2’. This affects partial matching of argument names!
Add manual support for scale transformations, needed for label construction and matching colour calculations.

ggspectra 0.3.13

CRAN release: 2024-09-13

Revise function autotitle() to better support collections of spectra and multiple spectra in long form.
Fix bug: Bad default y-limits in autoplot.calibration_spct() (bug introduced in version 0.3.12).
Fix bug: Error when attempting to plot cps_spct objects with multiple columns of cps data (bug introduced in version 0.3.12).
Fix previously inconsequential bug in autoplot() methods revealed by stricter checks.
In autoplot.response_spct() change default argument norm = "max" to norm = "update" for consistency with the other autoplot() methods and to avoid “surprising” users.
Revise all scales and the matching axis-label building functions by adding formal parameter axis.symbols with default given by R option ggspectra.axis.symbols.
Revise scales for transmittance, absorptance and reflectance and the matching axis-label building functions by adding formal parameter pc.out with default given by R option ggspectra.pc.out.
Revise all autoplot() methods so that the default argument for the pc.out can be set with R option ggspectra.pc.out.
Revise all autoplot() methods for objects of class generic_spct and derived so that summaries requested by arguments passed to parameter plot.data are computed for multiple spectra in long form like they are for collections of spectra.
Fix broken idfactor handling in autoplot() methods for objects of class generic_spct and derived.
Use in autoplot() methods a plotmath expression for the wavelength axis label, including lambda as symbol, for consistency with the labels of the y-axis.
Revise autoplot() methods to that the default argument for range can be set with R option ggspectra.wlrange.
The former vignette Plotting transformed data is now an article, no longer part of the package. It is replaced by the on-line only article Plotting transformed spectral data that includes new code examples using example data objects from package ‘photobiology’ (>= 0.11.1).
Add new on-line only article Animated plots of spectral data with examples that use package ‘gganimate’ together with ‘ggspectra’.

ggspectra 0.3.12

CRAN release: 2023-10-21

Improve how plots created with autoplot() look, e.g., limit number of digits in labels and improve some annotations in the case of multiple spectra.
Ensure that parameter ylim in autoplot() methods works correctly with any values passed as argument. Plots with non-default ylim values may change (for the better) and occasionally a plot made with defaults may look the same but not be identical.
Fix bug in autoplot.source_spct() introduced in version 0.3.10: bad handling of single waveband objects as argument to w.band.
Track bug fix in ‘photobiologyWavebands’, that updated the definition of PAR() (photosynthetically active radiation) as a BSWF (biological spectral weighting function). The labelling as PAR is now restored when plotting spectral photon response using the autoplot() method.
Replace use of “mu” (3bc) character by “micro” (0b5) in UTF-8, as Greek UTF-8 characters are not supported in all Linux versions (at CRAN’s request).

ggspectra 0.3.11

CRAN release: 2023-04-03

‘photobiology’ (>= 0.10.16) is needed as a bug in ‘photobiology’ (<= 0.10.15) can trigger an occasional error in autoplot().
Bug fix, attempt in autoplot() to use linetype aesthetic with more than the 13 supported levels. This changes plots with more than 13 spectra compared to earlier versions, but in these plots some spectra were missing. New behaviour is to use semi-transparent solid lines for more than 13 spectra.

ggspectra 0.3.10

CRAN release: 2023-01-15

Track bug fix in ‘photobiologyWavebands’, that updated the definition of PAR() (photosynthetically active radiation) as a BSWF (biological spectral weighting function). The previous definition of PAR() as a wavelength range returned a value that should be called “PAR” only when used to compute photon irradiance. This change does not affect the numerical values of energy irradiances or other spectral quantities, but now the waveband is labelled PhR instead of PAR in such cases.
Track changes in ‘photobiology’ 0.10.15.
Add sec_axis_energy_eV() and sec_axis_energy_J() to express wavelength as energy per photon, and sec_axis_wl() to allow a secondary wavelength axis with wavelengths expressed using a different scale factor than in the main axis.
Add scales scale_x_wavenumber_continuous(), scale_x_frequency_continuous(). scale_x_energy_eV_continuous() and scale_x_energy_J_continuous().
This version requires R (>= 4.1.0) and ‘ggplot2’ (>= 3.4.0).

ggspectra 0.3.9

CRAN release: 2022-10-16

Maintenance release for compatibility with ‘ggplot2’ >= 3.4.0.
Several bug fixes.
Revise all autoplot() methods adding formal parameter geom.

ggspectra 0.3.8

CRAN release: 2022-04-15

This update brings many improvements to autoplot() methods. These include enhanced capabilities for handling of normalized and scaled spectral data, as well as cosmetic tweaks to labels. It also tracks changes in packages ‘ggrepel’ (>= 0.9.1), ‘photobiology’ (>= 0.10.10) and ‘ggplot2’ (>= 3.3.3) and deprecation of functions in ‘tidyr’ (>= 1.0.0). The updated code depends on the revised normalize() function in ‘photobiology’ (>= 0.10.10) and on ‘ggrepel’ (>= 0.9.1).

Revise all autoplot() methods to support on-the-fly normalization internally using photobiology::normalize().
Revise autoplot() methods for source_spct, response_spct, filter_spct, reflector_spct, source_mspct, response_mspct, filter_mspct, and reflector_mspct so that if the data are already normalized, by default the normalization is updated according to the arguments passed to unit.out or plot.qty and range. (Update is possible only for objects normalized with ‘photobiology’ (>= 0.10.7). For objects created with earlier versions, the old behaviour of plotting spectra as is remains unchanged.)
Revise autoplot() method for object_mspct to force use of facets when plot.qty = "all" instead of forcing plotting of transmittance only.
Revise autoplot() method for object_mspct to correctly handle normalization of collections of spectra, one spectrum at a time, correcting a bug.
Revise all autoplot() methods to generate shorter y-axis labels also improving reporting of scaling and normalization when needed.
Revise all autoplot() methods to fix bug leading to bad object name in plot title due to delayed evaluation.
Add autoplot.cps_mspct() and autoplot.raw_mspct() methods.
Add support for faceting to all autoplot() methods for collections of spectra.
Revise all autoplot() methods for collections of spectra adding support for sum, prod, var, sd, and se as summaries. The support for these summaries depends on autoplot.generic_spct() which is still experimental and subject to change.
Update decoration() to track changes in ‘ggrepel’ (>= 0.9.1).
Update decoration() to use position_nudge() and position_nudge_repel() to displace labels instead of “off-range” justification.
Improve handling of multiple spectra in long form by ggplot() methods and by autotitle().
Remove direct dependency on ‘dplyr’.
Add to the documentation of all autoplot() methods an explanation of how to modify the default plot annotations and titles using arguments passed to parameter annotations. Also add see also links to related help pages.

Although this update should not break any code, the y-axis labels in plots returned by autoplot() methods have changed, in most cases only cosmetically to shorten them. In a few cases more significant edits correct problems.
Although this update should not break any code, the labels for peaks and valleys can be at a slightly different position than with earlier versions.
Although this update does not break any code, plots of collections of object spectra with normalization, will differ from earlier ones as member spectra are now normalized individually (this corrects an earlier bug!).

ggspectra 0.3.7

CRAN release: 2020-10-04

Track and profit from updated ‘photobiology’ (>= 0.10.4), with (>= 0.10.5) now required.
Use performance-optimized computation for colors from wavelengths.
Improve stat_wl_strip() performance by simplifying data before plotting.
Add support for plotting action spectra (preliminary).
Update y-axis scales to support scaled and normalized data.
Update y-scales to generate more compact axis labels and use IUPAC-recommended symbols.
Update x-axis- and y-axis scales to allow users to override the default label text.
Implement scale_y_Afr_continuous() for absorptance spectra.
Implement scale_y_mult_continuous() for calibration spectra.
Update autoplot() methods to generate more compact axis labels (preliminary).
Update autoplot.source_spct() method to to natively support facets (partial).
Update stat_wb_box() adding parameter box.height (default behavior unchanged).
Fix a documentation example that stopped working because of changes to ‘ggplot2’.

Although this update should not break any code, the plots created will in some cases differ slightly from those created with earlier versions. These changes affect the formatting of axis labels, and are readily visible.
Colors may differ very slightly while stat_wl_strip() draws fewer rectangles (in most cases these changes are barely visible).

ggspectra 0.3.6

CRAN release: 2020-04-28

Add support for computation of colors using other chromaticity coordinates than the color matching function (CMF) for human vision.
Revise for compatibility with ‘dplyr’ (>= 1.0.0).
Track changes in ‘photobiology’ 0.10.1.
Fix two bugs in ggplot() method for class object_spct.
Add stat_spikes(), useful for highlighting spikes.
Fitted peaks and valleys are now supported (experimental).
Rewrite stat_find_wls() using photobiology::wls_at_target().
Support new annotations "wls" and "wls.labels" in all autoplot() methods.
Update decoration() for this, and also other small tweaks.

Although this update should not break any code, the plots created will in many cases differ from those created with earlier versions. Changes only affect the text of labels.

ggspectra 0.3.5

CRAN release: 2020-01-16

Revise ggplot() methods so that the class and attributes of spectral objects are retained in the "data" member of the "gg" object. This allows use of methods specific to spectra in data transformations.
Track changes in ‘photobiology’ 0.9.30.

ggspectra 0.3.4

CRAN release: 2019-09-12

Update for code-breaking changes in ‘tidyr’ (>= 1.0.0).

ggspectra 0.3.3-1

Add convenience functions to make easier to modify plotting options: set_annotations_default() and set_w.band_default().
Add support for simultaneously adding and removing annotations from the current default by accepting lists of character vectors as argument for parameter annotations in autoplot() methods.
Add support in multiplot() for adding a title to the composite figure.
Add support for setting of the plot caption with autotitle() and as annotations in autoplot() methods. Make autotitle() a synonym of ggtitle_spct(), which is now deprecated.
Track changes in ‘photobiology’ (>= 0.9.28) adding support for "how.measured" attribute in plot titles, subtitles and captions.
Use a compute panel function instead of a compute group function in stat_wb_label(), stat_wb_box() and stat_wl_strip(), solving a bug affecting autoplot() methods when called with multiple spectra.

ggspectra 0.3.2

CRAN release: 2019-02-20

Move ‘ggplot2’ from Imports: to Depends: as the objects returned belong to classes defined in this package.
Move ‘photobiology’ from Imports: to Depends: as the objects accepted as input belong to classes defined in this package and is natural for users to want to use specialized methods to operate on them.
Define autoplot() methods as replacements for plot() methods, which are now deprecated. All documentation now uses autoplot().
As ‘ggplot2’ exports a generic for autoplot() and the expected returned value is a ggplot which matches the returned value of the methods defined here, we have renamed them to autoplot(). For backwards compatibility plot() methods remain available, but their use in new code is deprecated.

ggspectra 0.3.1

CRAN release: 2018-10-29

Fix major bug in plot() methods for source_spct and response_spct classes, that triggered errors in all cases when time.unit was not "second".
Add scale_y_s.e.irrad_log10() and scale_y_s.q.irrad_log10().
Test with ‘ggplot2’ version 3.1.0.

ggspectra 0.3.0

CRAN release: 2018-10-08

Change the names of some the values calculated by the stats defined in ‘ggspectra’ to avoid confusion with the names of ‘ggplot2’ aesthetics. This is a code breaking change!

Revise to track changes in ‘photobiology’ version 0.9.24 and ‘ggplot2’ 3.0.0, which are now required.

stat_label_peaks() and stat_label_valleys() now have a new parameter, label.fill which can be used to set the content of ..x.label.. and ..y.label.. for labels not labelled as peaks or valleys. The earlier use of "" is retained as default.
Add stat_find_wls() and stat_find_qtys(), two new statistics useful for highlighting and labelling features in spectra.
Add parameter ylim to all plot() methods.
Revise plot() methods to support objects with multiple spectra in long form.
Revise plot() methods to NOT display by default calculated summaries in annotations when a plot contains multiple spectra.
Revise plot() methods to retrieve and validate the name of the factor used to identify multiple spectra, using as default the value stored in the attribute "idfactor" implemented in ‘photobiology’ 0.9.21 and later.
Add autoplot() as an alias of plot() for spectra and collections of spectra.

ggspectra 0.2.4

Revise to track changes in ‘photobiology’ 0.9.20 to avoid spurious messages.

Add ggplot() method specialization for collections of spectra.
Add plot() method specializations for collections of spectra.

ggspectra 0.2.3

CRAN release: 2017-12-21

Track changes in package ‘photobiology’ 0.9.18.

Add plot.calibration_spct().
Add ggplot.calibration_spct().

Improve handling of plot titles.

Add utility function ggtitle_spct().
Update all plot() methods to allow flexible contents in automatic titles including setting of the time zone and format used for displaying time.

ggspectra 0.2.2

CRAN release: 2017-08-31

Track changes in package ‘photobiology’ 0.9.16 and 0.9.17. This among other improvements makes it easy to plot spectral absorptance. Expand y scale to expected range in all cases, but do not force these limits in any case when data exceeds them, except for absorbance for which the y scale is not expanded past 6 a.u. Add new annotation "boundaries" to highlight with horizontal line(s) the expected range of the plotted quantity, highlighting the limit(s) exceeded if data fall outside the expected/range. Add previously missing ggplot() method for class object_spct. Revise vignettes.

ggspectra 0.2.1

CRAN release: 2017-03-20

Track changes in package ‘photobiology’ 0.9.14. Add continuous scales with defaults suitable for spectral data, with support for automatic axis labels both as R-expressions and as LaTeX mark-up. Add utility functions for SI scale prefixes. Add utility functions for x-axis-labels and secondary x-axis. Add utility functions for y-axis-labels. Update User Guide (add examples of graphical comparison of multiple lists of wavebands).

ggspectra 0.2.0

CRAN release: 2016-12-22

Improve handling of annotations parameter in plot() methods. Add functions ggcolorchart() and black_or_white(). Add statistics stat_wb_box() and stat_wb_column() with "rect" as default geom and stat_wb_hbar() with "errorbarh" as default geom. Change default geom from "rect" to "text" in all the summary stats for spectra. Update stats with “text” as default geom to use an additional variable BW.color computed by black_or_white() as default mapping for color. As default geoms and color mapping have changed, this update can break existing code. Changes to plot() methods are backwards compatible but default color of some text labels is changed from "white" to "black" to improve readability, and fewer peaks and valleys are highlighted by default. In addition more ticks marks are used on the wavelength axis. Fix minor bugs in handling of color mapping. Update documentation.

ggspectra 0.1.12

CRAN release: 2016-11-16

Import ‘ggplot2’ in whole as only the most basic use of plot() methods would not require user access to ‘ggplot2’. Add stat_label_peaks() and stat_label_valleys() which are designed to fully take advantage of geom_text_repel() and geom_label_repel() as revised in package ‘ggrepel’ (>= 0.6.3). Change behaviour of plot() methods so that “illegal” values such as negative spectral irradiances or transmittances are plotted by default. Fix several minor bugs affecting plot() methods with certain non-default sets of annotations. Improve documentation and vignettes.

ggspectra 0.1.11

ggspectra 0.1.10

CRAN release: 2016-09-24

Add code to maintain same stacking order under ‘ggplot2’ 1.1.0, 2.0.0, 2.1.0, and 2.1.9000 in plot.object_spct().

ggspectra 0.1.9

Add support for na.rm to all plot() methods setting default to TRUE, and avoid triggering spurious warnings from internal code. Make default for parameter label.qty in plot methods dependent on whether data are expressed in absolute units or have been rescaled or normalized. Move from the ‘User Guide’ the sections on plot() methods creating a new vignette titled ‘Plot Methods’.

ggspectra 0.1.8

CRAN release: 2016-08-03

Add support for plot.qty = "absorptance" to plot.filter_spct(). Add support for plot.qty to plot.object_spct() with possible values: "all" or NULL (previous behaviour, and current default), "transmittance", "absorbance", "absorptance", and "reflectance". The new options plot only one quantity at a time as a line instead of the default area plot.

ggspectra 0.1.7

CRAN release: 2016-05-21

Add stat_wb_label(), stat_wb_e_irrad(), stat_wb_q_irrad(), stat_wb_e_sirrad(), and stat_wb_q_irrad(). Revise plot.raw_spct() to handle multiple "counts" columns. Revise plot.cps_spct() to handle multiple "cps" columns. Add text.size parameter to all plot() methods. Can be used to control the size of the font used for text decorations related to wavebands, peaks and valleys. Increase slightly the default font size for plot decorations, and decrease the number of peaks and valleys labelled by the plot() methods. Fix existing bug revealed by dplyr update. Fix bug in decoration() affecting plot.object_spct(). Fix other minor bugs.

ggspectra 0.1.6

CRAN release: 2016-02-06

(First CRAN release)

Clean documentation and code for CRAN submission. Add examples of plotting of waveband objects as these were removed from the vignette of package ‘photobiologyWavebands’.

ggspectra 0.1.5

Fix bug in documentation.

ggspectra 0.1.4

Improve documentation.

ggspectra 0.1.3

Remove wb_guide(). Remove wb_wb_summary(). Add stat_wb_mean(), stat_wb_total(), stat_wb_contribution(), stat_wb_relative(). Add stat_wb_irrad(), stat_wb_sirrad()

Implement 100% of the old functionality of the plot() methods, but without using any annotations. In other words, now all calculations work as expected with grouping and panels. Some aesthetics may require tweaking in the case of grouping.

Tested with packages ‘ggrepel’ and ‘cowplot’.

ggspectra 0.1.2

Add text explaining examples to User Guide.

Rename several stats and functions with more descriptive names.

stat_color_guide() -> stat_wl_strip()

stat_average() -> stat_wl_summary()

stat_waveband() -> stat_wb_summary()

color_guide() -> wl_guide()

waveband_guide() -> wb_guide()

ggspectra 0.1.1

Add multiplot() function (unchanged from package photobiologygg). Improve stat_waveband(). Add color_guide(), waveband_guide().

Add ggplot() methods for spectra, which use default mappings if mapping not explicitly supplied as argument to call.

Make plot() methods almost fully functional. "contribution" and "participation" summary values not yet implemented. Neither summaries for BSWFs. If requested these summaries will show as NaN (not a number) in the plots.

ggspectra 0.1.0

First preview version. Still with incomplete functionality.