SCpbur v2.0.2

General.

do_BeeSwarmPlot()

do_BoxPlot()

do_CopyNumberVariantPlot()

do_FeaturePlot()

do_ViolinPlot()

SCpubr v2.0.1

General

Removed functions

SCpubr::do_EnrichmentHeatmap

SCpubr v2.0.0

This major update focus on a complete re-implementation of all heatmap-based functions into ggplot2 instead of ComplexHeatmap. This will lead to many of the existing code to break. The trade-off between the difficulty of debug, expand and maintain the existing heatmap-based functions with regards to the capabilities ComplexHeatmap offers with regards to ggplot2 was not worthy.

All heatmap-specific parameters have been replaced with the overarching parameters that are used across functions. This decision was taking after a lot of thought, but ultimately, having all plots rely on ggplot2 makes it way more compatible to work with them together, to debug, and to further implement new ideas.

Many (except a few selected cases) of the functions that returned list of different plots have been modified to return a single (and most important/relevant) plot and the option to return the Seurat object with the data generated added to it has been implemented so that the user can still generate plots with it. This goes in line with the fact that having so many interconnected functions made it very difficult to expand on them, if needed, as the downstream effects will cascade to other functions as well.

Parameter renaming

New functions (available on the development build for extended texting)

Removed functions

General

SCpubr::do_AlluvialPlot

SCpubr::do_BarPlot

SCpubr::do_BeeSwarmPlot

SCpubr::do_BoxPlot

SCpubr::do_CorrelationPlot

SCpubr::do_CopyNumberVariantPlot()

SCpubr::do_DimPlot

SCpubr::do_DotPlot

SCpubr::do_EnrichmentHeatmap

SCpubr::do_ExpressionHeatmap

SCpubr::do_FeaturePlot

SCpubr::do_FunctionalAnnotationPlot

SCpubr::do_FunctionalAnnotationPlot

SCpubr::do_LigandReceptorPlot()

SCpubr::do_PathwayActivityPlot()

SCpubr::do_TFActivityPlot()

SCpubr v1.1.2

More hotfixes in unit tests to comply with CRAN checks.

SCpubr v1.1.1

Hotfixes in unit tests to comply with CRAN checks.

SCpubr v1.1.0

General

SCpubr::do_BeeSwarmPlot()

SCpubr::do_BarPlot()

SCpubr::do_BeeSwarmPlot()

SCpubr::do_BoxPlot()

SCpubr::do_CellularStatesPlot()

SCpubr::do_CorrelationPlot()

SCpubr::do_DimPlot()

SCpubr::do_EnrichmentHeatmap()

SCpubr::do_FeaturePlot()

SCpubr::do_GroupwiseDEPlot()

SCpubr::do_LigandReceptorPlot()

do_PathwayActivityPlot()

do_TFActivityPlot()

SCpubr::do_ViolinPlot()

SCpubr v1.0.4

SCpubr v1.0.3

General changes

SCpubr::do_DimPlot()

SCpubr::do_EnrichmentHeatmap()

SCpubr::do_FeaturePlot()

SCpubr::do_GeyserPlot()

SCpubr::do_RidgePlot()

SCpubr::do_ViolinPlot()

SCpubr v.1.0.3-dev-stable

SCpubr v1.0.2

General changes

SCpubr::do_CopyNumberVariantPlot

SCpubr::do_DimPlot()

SCpubr::do_DotPlot()

SCpubr::do_FeaturePlot()

SCpubr::do_GeyserPlot()

SCpubr::do_GroupwiseDEPlot()

SCpubr::do_LigandReceptorPlot() (development release)

SCpubr::do_RidgePlot()

SCpubr::do_ViolinPlot()

SCpubr v1.0.2-dev-stable

SCpubr v1.0.1

SCpubr v1.0.1-dev-stable

SCpubr v1.0.0

SCpubr v1.0.0-dev-stable

SCpubr 0.0.0.9000