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Version 0.4

pointillism 0.4.0 (2019-08-07)

Initial support for monocle3 cell_data_set class.

Major changes:

  • Reworked internal S4 function names.
  • Updated internal example data.
  • Moved cell-cycle and cell-type markers from Google Sheets here into the package internally at inst/extdata/markers/.
  • Working on preliminary support for monocle3 cell_data_set.

pointillism 0.4.1 (2019-08-12)

Minor changes:

  • Bug fix for gene symbols being sanitized by as.data.frame or as_tibble coercion inconsitently across R versions. Switched to using as coercion from DataFrame to data.frame instead.
  • Improved message consistency, removing use of backticks in favor of single quotes, which is now the convention across basejump.
  • Lintr check fixes.

pointillism 0.4.2 (2019-09-04)

Major changes:

  • Reworked internal code to remove dplyr, magrittr, rlang, tibble, and tidyr dependencies. Consistently using base R and Bioconductor S4 methods internally instead, working primarily with DataFrame instead of tbl_df.

pointillism 0.4.3 (2019-10-26)

Minor changes:

  • Bug fix for legacy Seurat objects created via pointillism with named rownames containing gene identifiers mapped to the gene symbols. Now the coercion method for Seurat to SingleCellExperiment checks for this and sanitizes the names automatically so the resulting SingleCellExperiment is valid.

pointillism 0.4.4 (2019-10-30)

Bioconductor 3.10 compatibility fixes.

pointillism 0.4.5 (2020-01-03)

Major changes:

  • normalize: reworked internal code to reflect changes in scater package. Instead of calling normalizeSCE or normalize internally, normalizeCounts is the recommended method for returning normcounts and logcounts assays that can be slotted in assays of the SingleCellExperiment object.
  • Deprecated plotDot in favor of plotDots (note plural spelling change). This reads better and improves consistency with conventions used in scater.

Minor changes:

  • Removed user-defined option to reduce verbosity, where applicable. If these functions are too noisy, we’ll tone it down in the future.

pointillism 0.4.6 (2020-01-20)

Minor changes:

  • Reworked NAMESPACE to support migration of bioverbs package to AcidGenerics.

pointillism 0.4.7 (2020-01-30)

Minor changes:

  • Now using cli package for messages.
  • Updated basejump dependencies.

pointillism 0.4.8 (2020-02-20)

Major changes:

  • plotReducedDim, plotMarker: Changed title handling support. Switched from using title argument in favor of labels, which better matches the conventions now used in AcidPlots.

Minor changes:

  • Seurat methods now show resolution parameter used to map idents, where applicable. Currently this applies to plotReducedDim family of functions.

pointillism 0.4.9 (2020-02-21)

Minor changes:

  • runZinbwave: Updated internal zinbwave code to be compatible with Bioconductor 3.11 release.
  • Updated test data.

pointillism 0.4.10 (2020-06-11)

New functions:

  • plotStackedBarPlot: Added support for quickly generating stacked bar plots of cluster frequencies.

Minor changes:

  • Dependency updates.

pointillism 0.4.11 (2020-06-27)

Major changes:

  • runSeurat: Changed umapMethod default from “umap-learn” to “uwot”. I’m having trouble getting the latest version of umap-learn (0.4.4) to play nicely with Seurat (3.1.5) via reticulate (1.16). Note that additional internal arguments are now passed to Seurat::RunUMAP when necessary.

pointillism 0.4.12 (2020-07-23)

Minor changes:

  • Maintenance release, updating R dependency to 4.0.

pointillism 0.4.13 (2020-08-04)

Minor changes:

  • Removed patrick dependency for unit tests.
  • Updated other package dependency versions.
  • Wrapped suppression calls with { where necessary.

pointillism 0.4.14 (2020-10-12)

Minor changes:

  • Renamed alpha argument to alphaThreshold, matching naming conventions used in other Acid Genomics packages. Applies to marker class objects.
  • Updated dependencies to support naming changes in Acid Genomics packages.