This version (0.3.2) adds as new features scales and statistics that help with the creation of volcano and quadrant plots, such as used with transcriptomics and metabolomics data. A few rough edges remaining in the features added in versions 0.3.0. and 0.3.1 have been polished out. Two issues raised in Bitbucket about the documentation, highlighted some incomplete explanations. These explanations have now been expanded. One important change to the documentation of statistics whose returned values may change depending on arguments is the addition of an example of the use of geom_debug() from package ‘gginnards’ showing how to print to the R console the data returned by statistics, which is the input received by the paired geometries. The User Guide needs still some work, scheduled for the next release. Package documentation is available at https://docs.r4photobiology.info/ggpmisc/ as a web site.
Plots created using the new statistics and scales are shown below. In the quadrant plot, which observations were labelled and highlighted was decided automatically based on local 2D density. Counts for each quadrant are computed on the fly. As the plot is non-the-less created using the grammar of graphics, little if any of the flexibility of ‘ggplot2’ is lost.
NOTE: The new version of ‘ggpmisc’ is on its way to CRAN.
This update includes a fix for a bug affecting autoplot() methods in the case of plotting multiple spectra in the same plot. It also includes improvements to the easy of use through the addition new or enhancements to existing convenience methods and functions. The required version of ‘photobiology’ is now 0.9.28 or higher.
The changes from version 0.3.2, the current CRAN release, are:
Make autotitle() the recommended method and deprecate the use of ggtitle_spct(), which remains available for backwards compatibility.
Enhance autotitle() to optionally set the caption in addition to title and subtitle of a plot.
Add support for setting of the plot caption controlled with the annotations argument of autoplot() methods.
Add convenience functions to make easier to modify default arguments used by autoplot() methods through R 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 in addition to character vectors as argument for parameter annotations in autoplot() methods.
Add support in multiplot() function for adding a title to the composite figure.
Track changes in ‘photobiology’ (>= 0.9.28) adding support for using the "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.
The justification for renaming the ggtitle_spct() function to autotitle() is that the new name is consistent with autoplot() and autolayer() in taking an R object of a specific class as first argument and automatically extracting the information from it.
After the previous major update to ‘ggpmisc’ (0.3.0), a follow up (0.3.1) with multiple new features and smoothed rough edges for some of the features added in version 3.0.0. Package documentation is available at https://docs.r4photobiology.info/ggpmisc/ as a web site.
The enhancements in this and the previous update to ‘ggpmisc’ are made possible by changes to ‘ggplot2’ (>= 3.0.0) made while adding support for sf (simple features).
The functions in ‘ggpmisc’ (>= 0.3.1) are related to different kinds of annotations and insets in ggplots. Annotations of plots with fitted-model equations, fit diagnosis, ANOVA and summary tables, highlighting and labelling of peaks and valleys in curves, and local density-based highlighting or labelling in scatter plots. Additionally specializations of the ggplot() constructor allow on-the-fly conversion of time-series. Two new geoms join geom_table() added in version 0.3.0, geom_plot() and geom_grob(). These three geoms make it possible to add tables, ggplots and arbitrary graphical objects (grobs) as insets to plots respecting the the Grammar of Graphics paradigm.
A set of new geometries produce marginal annotations: geom_x_margin_point(), geom_y_margin_point(), geom_x_margin_arrow(), geom_y_margin_arrow(), geom_x_margin_grob() and geom_y_margin_grob().
Another novel feature is based on the addition of two new aesthetics npcx and npcy, the corresponding scales scale_npcx_continuous() and scale_npcy_continuous(), and several new geometries that make use of then: geom_text_npc(), geom_label_npc(), geom_table_npc(), geom_plot_npc() and geom_grob_npc(). These allow to position insets and annotations relative to the dimensions of the plotting area instead of using native data units. Using "npc" units is more natural for labels or insets that are not directly related to data but that look better if positioned consistently across multiple panels or multiple separately produced plots. One improvement to the stats from earlier versions of ‘ggpmisc’ is the use of these new geoms to achieve more consistent location for insets and labels.
As in the announcement of the previous version, I have included some example plots taken from the documentation of the package. In all cases annotations are generated automatically, but formatting is flexible.
NOTE: The new version of ‘ggpmisc’ will be soon submitted to CRAN .
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional measurement methods.
Update acq_irrad_interactive() adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra.
Add pre-built calibrations and methods for additional FLAME-S instruments.
Improve algorithm for automatic tuning of integration time to achieve faster convergence.
Fix various minor bugs.
Test against OmniDriver 1.2.56
Update read_ooov_files() for compatibility with ‘readr’ >= 1.2.0 which is now required
Add support for measurement of pulsed light sources (under development)
The new features described below are under development, subject to change without previous notice and not yet well tested!! (double-check any results and please report any bugs by raising an issue!)
Implement support for measuring output from xenon flashes, including use of such flashes as light sources for measurement of spectral transmittance and reflectance. Use of multiple exposures per integration is also supported and the number of exposures stored as metadata is used during later processing. In the case of pulsed light sources the first conversion of RAW spectra is into counts per exposure, and instead of spectral irradiance spectral fluence per exposure is computed. All changes are backwards compatible with raw data acquired with earlier versions of ‘ooacquire’ and the user interface remains unaltered for the measurement of continuous light sources.
Add function acq_fluence_interactive() for measuring spectral fluence of pulsed light sources.
Add acq_fraction_pulsed_interactive() for measuring transmittance and reflectance using a pulsed light source.
from sources retrieved from the Git repository at Bitbucket.
devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.6")
devtools::install_bitbucket("aphalo/photobiology") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/photobiologyWavebands") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/ggspectra") # only if not automatically installed/updated