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.

acidplots 0.2.6 (2019-07-18)

Minor changes

  • plotCountsPerBiotype: Internal tidyeval bug fix for call to dplyr::top_n. Previously, the n argument supported direct variable input, but now it must be unquoted, due to change in underlying rlang engine following the 0.4 update.

acidplots 0.2.7 (2019-07-23)

New functions

  • plotCountsCorrelation and plotCountsCorrelationHeatmap: New functions optimized for plotting correlation between gene expression matrices. Particularly useful for comparing pseudoaligned vs. aligned counts, which is implemented in the new bcbioRNASeq package update.

Minor changes

  • Improved naming consistency of internal S4 functions.
  • Updated basejump dependencies.

acidplots 0.2.8 (2019-07-29)

Minor changes

  • Improved warning suppression for partial match in pheatmap calls.
  • Improved documentation.
  • Improving automatic plot title and label handling with new makeLabel and makeTitle functions from syntactic update.

acidplots 0.2.9 (2019-07-30)

Minor changes

  • Updated basejump dependency versions.
  • Updated some unit tests to reflect RangedSummarizedExperiment example update in acidtest package.

acidplots 0.2.10 (2019-08-06)

Minor changes

  • Improved documentation consistency by importing shared parameter roxygen from the new acidroxygen package.
  • Updated basejump dependency versions.

acidplots 0.2.11 (2019-08-12)

Major changes

  • Migrated some QC plotting functions previously defined in bcbioSingleCell package. This makes it possible to share the code for new Chromium package, designed for importing single cell RNA-seq data from 10X Genomics.

acidplots 0.2.12 (2019-08-20)

Minor changes

  • Improved consistency of internal tibble handling inside plot functions.
  • Updated basejump dependency versions.

acidplots 0.2.13 (2019-08-21)

Minor changes

  • plotPCA: Improved automatic ntop argument handling when passing in a value greater than the number or features (rows) defined in the object.
  • Improved documentation for SingleCellExperiment methods that need to average or aggregate expression at sample level.
  • Removed dplyr and magrittr dependencies.

acidplots 0.2.14 (2019-08-27)

Minor changes

  • plotCountsPerFeature: Renamed formals to match conventions in new basejump melt methods.
  • Updated basejump dependencies and NAMESPACE.
  • Tightened up if/then checks, ensuring boolean flag return.
  • Improved some working examples and unit tests.

acidplots 0.2.15 (2019-09-13)

Major changes

  • acid_theme_dracula: New dark mode theme supporting Dracula color palette.
  • Exporting color palette vectors: lightPalette, darkPalette, draculaPalette, iOSLightPalette, iOSDarkPalette, macOSLightPalette, macOSDarkPalette.
  • synesthesia: Simplified color palette to use purple, blue, green, orange. User can tweak the palette using a new palette argument.

acidplots 0.2.16 (2019-09-16)

Major changes

  • Replaced title argument with labels argument for functions that render plots using ggplot2.
  • Now exporting matchLabels function, that handles internal ggplot2 label matching, and auto-populates with defaults in formal argument.
  • Using “samplesAxis” and “countsAxis” labels for ggplot2 return that support multiple geoms. Consider a similar approach for QC metric plots.

Minor changes

  • Simplified internal handoff from SingleCellExperiment S4 methods to SummarizedExperiment, using standard ... passthrough instead of relying upon matchArgsToDoCall.
  • Improved color palette consistency in plotting functions.