acidplots 0.2.0 (2019-04-22)

Reworked package, consolidating previous minimalism and firestarter packages.

New functions

  • synesthesia color 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.
  • Renamed ggplot2 themes: acid_theme_light, acid_theme_dark.

Major changes

  • All ggplot2 geoms and transformations (ggproto functions) now consistently use acid_ as a prefix.

Minor changes

  • plotCountsPerBiotype and plotCountsPerBroadClass now support title.

Deprecations

  • plotCountsPerGene has been renamed to plotCountsPerFeature.
  • plotGenesDetected has been renamed to plotFeaturesDetected.
  • Deprecated theme_paperwhite and theme_midnight in favor of acid_theme_light and acid_theme_dark.

acidplots 0.2.1 (2019-04-25)

New functions

  • New gradient palette functions: purpleOrange, blueYellow.
  • Remove gplots package from imports.

Major changes

  • plotHeatmap now supports automatic color calculation when breaks argument is defined. Also improved support for legendBreaks.

Minor changes

  • Fix .pheatmapColorPalette internal check for color, which requires n argument, rather than assuming positional variable.
  • plotCountsPerFeature: Improve the count subtitle.
  • S4 generic reexport documentation fixes.
  • Miscellaneous documentation fixes.

acidplots 0.2.2 (2019-04-26)

Major changes

  • Now importing upset function from UpSetR, with modified formals, so we can easily call this from other packages, including DESeqAnalysis.

acidplots 0.2.3 (2019-05-05)

Major changes

  • Now pinned against R >= 3.5.

acidplots 0.2.4 (2019-05-08)

Minor changes

  • Improved log2 and log10 axis scale handling for plotCountsPerBiotype and plotCountsPerBroadClass. Previously, the breaks argument was defined in internal scale_y_continuous ggplot2 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.

acidplots 0.2.5 (2019-07-17)

Minor changes

  • upset: Compatibility update for UpSetR v1.4 release.
  • Compatibility fixes for basejump v0.10.11 release.