CHANGELOG.md

Upcoming

[1.0.12] - 2024 February 26

• Makevars fixes
• Updated README URL to YouTube tutorial for CRAN

[1.0.11] - 2023 June 25

• Minor bug fix for plotEmbedding, issue 139
• Remove C++11 flags

[1.0.10] - 2022 April 19

• Removed debugging lines mistakenly included in the release. Re-versioning.

[1.0.9] - 2022 March 2

• Fixed self$plotGeneHeatmap() to work with NA/NaN/Inf values
• Fixed bug with self$plotDiffGeneHeatmap(); access list elements
• Use inherits() instead of class() comparisons for CRAN

[1.0.8] - 2021 December 12

• Fixed indexing error in writing the *csv files for the p2 app grids (e.g. "Gene sets in Aspect")

[1.0.7] - 2021 November 14

• Added ability to export data in grids as *csv
• Small revisions to docs

[1.0.6] - 2021 October 06

• Fixed read10xMatrix() to work with new 10x files

[1.0.5] - 2021 August 11

Changed

• Removed the vignettes and dependency on the drat repository at https://github.com/kharchenkolab/p2data

[1.0.4] - 2021 June 28

Changed

• Fix self$counts <- counts
• Fix Knn() in pagoda2WebApp.R

[1.0.3] - 2021 May 01

Changed

• Removed jsDist() as it's in sccore
• Removed multi2dend() as it's in sccore
• Removed strong dependency for p2data

[1.0.2] - 2021 March 03

Changed

• Revised vignettes figures for the HTML tutorial

[1.0.1] - 2021 February 25

Added

• Returned copy constructor

Changed

• Fixed read10xMatrix() function
• Updated Dockerfile
• Fixed 'batch' param in Pagoda2 constructor

[1.0.0] - 2021 January 28

• The package was edited extensively to upload to CRAN

Added

• read10xMatrix() was added
• more detailed roxygen2 docs
• Use p2data and drat to install PBMC data for pagoda2 vignettes and examples. This was largely due to the size of the data and CRAN rules. Refer to https://github.com/kharchenkolab/p2data & https://github.com/kharchenkolab/drat

Changed

• The classes Pagoda2() and p2ViewPagodaApp() are now R6 classes; note pagoda2WebApp() is still a reference class as it depends on Rook
• Vignettes revised
• revise message() spacing for verbose statements
• various changes for CRAN, e.g. par(), removing calls to installed.packages(), etc.

[0.1.4] - 2020 October 05

Added

• added p2app4conos() for rendering Conos to pagoda2 application
• README edits
• vignettes edits

[0.1.3] - 2020 October 02

Added

• Makefile.win, Makevars.win
• Made OpenMP headers conditional

Changed

• Now should (natively) install on Mac OS for all users

[0.1.2] - 2020 September 24

Added

• Parameter gene in plotEmbedding for coloring by normalized counts

Changed

• Using sccore plotting system for embedding plot. 3d plots aren't supported anymore.
• Added LICENSE (July 2020)
• Changed std::cout to Rcpp::Rcout (July 2020)

[0.1.1] - 2019 November 26

Added

• Function p2.generate.go now supports arbitrary annotations
• added use.raw.variance
• UMAP and UMAP_graph embedding support
• Specificity metrics to getDifferentialGenes

Changed

• removed negative value check to allow for custom starting values
• Fixed problem with duplicated observations during t-SNE estimation
• Added option var.scale to calculatePcaReduction, which allow to disable variance scaling on counts

[0.1.0] - 2019 April 20

Added

• Parameter min.transcripts.per.cell

Removed

• Removed dependencies on boost, GSL and Cairo

Fixed

• Moved GO.db to Suggests
• Added BioConductor dependencies to DESCRIPTION