pointillism 0.2.4 (2019-01-24)

pointillism 0.2.3 (2019-01-08)

pointillism 0.2.2 (2018-12-22)

pointillism 0.2.1 (2018-12-01)

pointillism 0.2.0 (2018-11-15)

pointilism 0.1.3 (2018-08-26)

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.

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.

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 0.1.0 (2018-08-10)

  • Initial release.