This is a documentation only update, with the following enhancements compared to ‘gginnards’ 0.0.2.
Expand the User Guide.
Revise documentation adding examples and correcting minor errors.
Rewrite README in R markdown adding examples.
Documentation web site at http://docs.r4photobiology.info/gginnards/ includes all help pages, with output from all examples, and vignettes in HTML format. NOTE: The new version of the package has been submitted to CRAN.
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.
Three of my packages needed updates due to code-breaking changes introduced in ‘tidyr’ 1.0.0, an update which will soon be submitted to CRAN by its authors. I received warning e-mails only about ‘photobiologyInOut’, which I have updated and submitted to CRAN some time ago. More recently I have noticed that ‘ggspectra’ had also to be updated and this required an update to ‘photobiology’. ‘ggspectra’ 0.3.4 is ready to be submitted to CRAN as soon as ‘photobiology’ 0.9.29 is built on CRAN servers.
If you have been using ‘tidyr’ in your scripts, you may need to update them. The required edits are rather small but can come as a surprise, which is why I am writing this post.