pointillism 0.1.0 (2018-08-10)

  • Initial release.

pointillism 0.1.1 (2018-08-20)

New functions

  • Now exporting runZinbwave and hasZinbwave, which were previously internal functions called by diffExp.

Minor changes

  • Improved internal handling of assays for objects that have zinbwave calculations applied. Now it doesn’t attempt to keep only the counts assay.

pointillism 0.1.2 (2018-08-22)

New functions

  • clusterID: S4 generic that returns the cell cluster identity mappings as a factor for all cells.
  • findMarkers: Utility function that wraps diffExp to identify cluster- specific genes across all clusters.

Minor changes

  • Converted runZinbwave to an S4 method that works on SingleCellExperiment. For seurat objects, coerce to SingleCellExperiment before calculating weights.
  • plotDot now uses default ggplot2 color scale, unless specified.
  • plotReducedDim, plotMarker: theme_paperwhite is no longer used by default. Removed grid and aspectRatio arguments to simplify ggplot2 code handling.

pointilism 0.1.3 (2018-09-19)

Major changes

  • as(seurat, "SingleCellExperiment") now returns scaleData in assays, along with varGenes in metadata and ensures that colData and rowRanges are sanitized into camel case using the camel function internally.

Minor changes

  • Removed convertGenesToSymbols support for seurat class. Coerce genes to symbols manually prior to seurat coercion from SingleCellExperiment.
  • clusterID: improved consistency between SingleCellExperiment and seurat methods, which now both work on colData.
  • Improved internal fetchData calls to use camel case for consistency.
  • plotFeature now sanitizes the features argument into camel case internally, for more consistent matching.
  • plotReducedDim now uses camel case formatting for axis labels.
  • Removed unnecessary legacy .minimalAxis constructor.
  • metadata<- assignment method now stashes directly into object@misc for seurat class.
  • Updated example data script and resaved.