pointillism 0.3.0 (2019-04-16)

Major changes

  • Updated S4 methods to support Seurat v3 release. Also updated imports from Seurat to reflect v3 change: GetAssayData, Stdev, VariableFeatures.
  • Now importing S3 coercion methods from Seurat: as.SingleCellExperiment. as.Seurat, which coerces SingleCellExperiment, isn’t particularly helpful because it requires logcounts slot to be defined in SCE. We’re calling CreateSeuratObject internally in our S4 coercion method instead, so that any SCE object can be easily coerced to a Seurat object.
  • Resaved and renamed example data: seurat, seurat_all_markers, seurat_known_markers.
  • Overhauled R Markdown templates.

Minor changes

  • Added preliminary plotCellTypesPerCluster method support. Need to test this out on larger datasets with many samples per cluster.
  • Switched Travis CI configuration to use Docker image.
  • Added some additional comments regarding reticulate umap-learn configuration required to run Seurat::RunUMAP. Consider putting some information in the README, since there is a lot of misinformation on GitHub regarding proper UMAP configuration.
  • Removed setOldClass definitions for session_info and package_version.
  • Renamed as-methods.R to coerce-methods.R, matching bsaejump conventions.
  • cellCountsPerCluster: Improved internal interestingGroups handling.
  • Reworked reexport method for S4 generics imported from bioverbs package.

pointillism 0.3.1 (2019-04-23)

Minor changes

  • Switch to importing ggplot2 code from new acidplots package. Recommended default ggplot2 themes are now named acid_theme_light and acid_theme_dark.
  • Consolidated S4 class and generator function documentation into single Rd files, where applicable.

pointillism 0.3.2 (2019-04-25)

Minor changes

  • S4 generic reexport documentation fixes.