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Version 0.2

pointillism 0.2.0 (2018-11-15)

New functions:

  • CellCycleMarkers, CellTypeMarkers, and KnownMarkers generator functions.
  • cellTypesPerCluster S4 generic.
  • topMarkers S4 generic.
  • New functions to import sheets from Google: importCellCycleMarkersFromGoogle and importCellTypeMarkersFromGoogle. These may be removed in a future update, in favor of simply using CSV files managed in the package. We’ve also included a helpful makeCellTypeMarkersFromGoogle utility function.
  • SeuratMarkers: New function for returning sanitized Seurat marker output.
  • SeuratMarkersPerCluster: Returns an S4 class split by cluster.

Major changes:

  • Improved S4 coercion methods. Added support for CellCycleMarkers to tbl_df, CellTypeMarkers to tbl_df, and SeuratMarkersPerCluster to tbl_df.
  • Reworked internal code for plotFeature.
  • plotKnownMarkers is now exported instead of plotKnownMarkersDetected.
  • Improved formals (and consistency) for dimensional reduction plotting functions. This applies to plotReducedDim, plotTSNE, plotPCA, and plotUMAP.
  • runZinbwave: Improved internal code and weight handling.

Minor changes:

  • Reworked validity checks for S4 classes.
  • Reworked internal assert checks. Refer to .assertIsBPPARAM, for example.
  • Broke out S4 methods into internal functions, where applicable. Refer to cellCountsPerCluster.SingleCellExperiment, for example.
  • Cleaned up example datasets. Removed known_markers_detected_small and sce_small.
  • diffExp: Reorganized and reworked internal code that uses zinbwave.
  • Reworked and improved Seurat-to-SingleCell interconversion support. Refer to seurat-SingleCellExperiment-methods for details.

Deprecations:

These functions have been deprecated: knownMarkers, knownMarkersDetected, plotKnownMarkersDetected, readCellTypeMarkers, sanitizeMarkers.

pointillism 0.2.1 (2018-12-01)

Major changes:

  • Reworked internal code to use goalie package for assert checks.
  • SeuratMarkersPerCluster: Simplified S4 validity checks.
  • Improved show methods for S4 classes: CellCycleMarkers, CellTypeMarkers.
  • Added summary method support for SeuratMarkers, SeuratMarkersPerCluster.

Minor changes:

  • Miscellaneous documentation improvements and fixes.
  • Reworked internal code shared between CellCycleMarkers and CellTypeMarkers S4 generator functions.
  • SeuratMarkers: Overhauled internal code, moving from .seuratMarkers internal function. Refer to SeuratMarkers.R for details.
  • Added AppVeyor CI support.

pointillism 0.2.2 (2018-12-22)

Major changes:

  • Migrated S4 generics to bioverbs package.
  • Finish migrating assert checks to goalie package.

Minor changes:

  • Moved S4 validity checks into setClass call, rather than using a separate setValidity call. Refer to AllClasses.R for details.
  • Removed makeCellTypeMarkersFromGoogle utility function.

pointillism 0.2.3 (2019-01-08)

Minor changes:

  • Comment out lines to pass lintr checks.
  • Split out imports into a separate imports.R file.
  • Added nullOK flag in assert checks, where applicable. See isGGScale, for example.

pointillism 0.2.4 (2019-01-24)

Minor changes:

  • SeuratMarkersPerCluster to tbl_df coerce needed a decode call to properly handling gene-to-symbol mappings with run-length encoding (Rle).

pointillism 0.2.5 (2019-04-01)

Major changes:

  • Migrated code to Acid Genomics.
  • Made runZinbwave defunct. No longer recommending zinbwave calculations for droplet single-cell RNA-seq.
  • ggplot2 themes theme_paperwhite and theme_midnight are now imported from minimalism package instead of basejump.