Reworked package, consolidating previous minimalism and firestarter packages.
synesthesiacolor palette functions.
acid_coord_flip: Intelligently puts samples at the top of the Y axis when flipped. Particularly useful for barplots.
acid_pretty_breaks: Attempt to improve
scales::pretty_breaks, using an approach more similar to the base plot engine.
ggprotofunctions) now consistently use
acid_as a prefix.
plotHeatmapnow supports automatic color calculation when
breaksargument is defined. Also improved support for
upsetfunction from UpSetR, with modified formals, so we can easily call this from other packages, including DESeqAnalysis.
plotCountsPerBroadClass. Previously, the
breaksargument was defined in internal
scale_y_continuousggplot2 call, but this doesn’t perform well for many RNA-seq datasets at log2 scale. Instead, it’s better to log2 scale the data first and then simplify indicate log2 on the y axis title.
plotCountsPerFeature: Improved custom color handling for density geom. Removed violin geom support but added jitter geom support. The violin plot method doesn’t scale well for multiple samples, and the boxplot is visually easier to interpret for this metric, in general.