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

• Increased the cell size of all heatmap-based functions from 5 to 8.
• Decreased the thickness of frame and ticks of all ggplot2-based continuous legends to retrieve a similar behavior as in previous versions of ggplot2, as with the new update, the overall thickness of the frame and ticks increased, probably due to the changes related to element_line,
• Added five new functions: do_AlluvialPlot(), do_AzimuthAnalysisPlot(), do_ExpressionHeatmap(), do_GroupedGOTermPlot() and do_FunctionalAnnotationPlot().
• Added legend.ncol, legend.nrow, legend.title and legend.byrow to as many functions as possible to further customize legend appearance.

SCpubr::do_BeeSwarmPlot()

• Added min.cutoff and max.cutoff parameter.
• Added ticks to the plot, that were missing.
• Added missing axes titles.
• Added viridis_direction parameter to control how the continuous color scale is formed.
• Added return_object parameter to return the Seurat object with the enrichment scores computed.
• Added BoxPlots, BeeSwarmPlots and ViolinPlots to the possible outputs the user can choose from.
• Make legend.position conditional of whether continuous_feature is set to TRUE. If it is false, legend is not displayed unless the user specifies otherwise.

SCpubr::do_BarPlot()

• Fixed a bug in which axes titles were not displaying correctly under certain combinations of flip and split.by.
• Fixed a bug in which x_lab and y_lab would not rotate accordingly when using flip = TRUE.

SCpubr::do_BeeSwarmPlot()

• Adapted the code to the new 0.7.1 version of the package, thus deprecating the groupOnX parameter of geom_quarirandom. This will likely affect users with a lower version.
• A warning has been placed for the users in lower versions of the need to upgrade to 0.7.1.
• This changes are subject to the new behaviors/deprecations of ggplot2 and ggplot2.

SCpubr::do_BoxPlot()

• Set assay to NULL and will default to the default assay in the seurat object.

SCpubr::do_CellularStatesPlot()

• Fixed a bug that prevented FeaturePlots to have symmetrical axes with respect to the main plot.

SCpubr::do_CorrelationPlot()

• Added viridis_direction parameter.

SCpubr::do_DimPlot()

• Fixed a bug in which the legend title will not show up in regular basic plots even though the parameter legend.title was used.
• Completely reformatted the way split.by works, so that now only one legend is displayed for the whole group and cells have border.
• Added label.size and label.box parameters for further customize the appearance of the plot when using label = TRUE.
• Changed repel to FALSE by default.

SCpubr::do_EnrichmentHeatmap()

• Fixed a bug in the code that prevented the feature plots and the geyser plots to be computed if the input gene list was not a named list of genes.
• Added flavor = "AUCell", that lets the user compute AUCell scoring of the gene sets.
• Added the option to query multiple group.by parameters at the same time.
• Fixed a bug in the code that prevented multiple outputs with different values of group.by to be returned properly, leading to the last value of group.by replacing all the rest.

SCpubr::do_FeaturePlot()

• Added label, label.size and label.color parameter to reproduce the same behavior as in Seurat::FeaturePlot().

SCpubr::do_GroupwiseDEPlot()

• Set assay to NULL and will default to the default assay in the seurat object.

SCpubr::do_LigandReceptorPlot()

• Added arrange_interactions_by to control how output interactions are arranged (either by aggregate_rank, specificity, magnitude or a combination of magnitude and specificity).
• Added sort_interactions_alphabetically to control whether the output dotplot has the interactions ordered alphabetically or as they come in the original matrix (meaning, they follow the arrangement specified in arrange_interactions_by). ((liana’s issue #72))

do_PathwayActivityPlot()

• Added a fix in which when enforce_symmetry is set to FALSE, then the color scale turns into a viridis-based one instead of a two-color gradient scale.

do_TFActivityPlot()

• Added a fix in which when enforce_symmetry is set to FALSE, then the color scale turns into a viridis-based one instead of a two-color gradient scale.

SCpubr::do_ViolinPlot()

• Fixed a bug in the code in which no different colors could be passed to colors.use.
• Reduced default line width from 1 to 0.5.

SCpubr v1.0.4

• Hotfix for v1.0.3 in which do_GeyserPlot with categorical variables had a bug that mapped the legend to the continuous axis.

SCpubr v1.0.3

General changes

• Added min.cutoff and max.cutoff parameter to effectively subset the color scale and remove the effect of extreme outliers in all ComplexHeatmap-based functions.
• Added min.cutoff and max.cutoff parameter to effectively subset the color scale and remove the effect of extreme outliers in all ggplot2-based functions susceptible to be biased by outliers.

SCpubr::do_DimPlot()

• Implemented a change in which when using split.by and group.by in combination, the cells colored on top of the UMAP also have a border.
• Implemented a bug-fix in which when using split.by and group.by in combination, the extra new layers would not raster if raster = TRUE.
• Implemented a bug-fix in which when using split.by and group.by in combination, no plots will appear if ncol is set.
• Implemented a new feature to add density line contours using plot_density_contour.
• Implemented the conditional use of raster.dpi to Seurat versions higher or equal to 4.1.0.

SCpubr::do_EnrichmentHeatmap()

• Implemented a bug fix for internal checks in the function.
• Added plot_FeaturePlots and plot_GeyserPlots to also report the enrichment scores in a gene set-based manner.
• Added flavor parameter, that accepts Seurat and UCell to allow for different enrichment scoring methods. It requires R 4.2.0 to run.
• Renamed symmetrical_scale to enforce_symmetry to have a greater coherence across functions.

SCpubr::do_FeaturePlot()

• Implemented a new feature to add density line contours using plot_density_contour.
• Implemented the conditional use of raster.dpi to Seurat versions higher or equal to 4.1.0.

SCpubr::do_GeyserPlot()

• Fixed bug in which internal parameter names made it to the X axis title.
• Removed color.by implementation due to it being very buggy. This will be re-implemented in a future patch.

SCpubr::do_RidgePlot()

• Implemented a bug-fix in which using assay = "RNA" or, in fact, any other assay rather than SCT will result in an error.

SCpubr::do_ViolinPlot()

• Corrected a bug in which legend title when using split.by was an actual line of code.
• Added legend.title parameter to control the title of the legend.

SCpubr v.1.0.3-dev-stable

• Same as v1.0.3, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

SCpubr v1.0.2

General changes

• Change color palette when using enforce_symmetry = TRUE to have the middle color as grey95 instead of the previous one, which made middle values seem closer to the positive end of the scale.
• Modified internal structure of all functions to abide with tidyselect v1.2.0 lifecycle modifications.
• Modified rotate_x_axis_labels parameter in all functions that made use of it. Now, instead of accepting a logical, accepts a numeric: either 0, 45 or 90, corresponding to the degrees in which the X axis labels should be rotated. (#5)

SCpubr::do_CopyNumberVariantPlot

• Modified the code for SCpubr::do_CopyNumberVariantPlot to also report results for the whole chromosome as well as for each chromosome arm.
• Include the verbose argument to SCpubr::do_CopyNumberVariantPlot to silence the messages when there are not enough genes in the chromosome to perform the analysis.

SCpubr::do_DimPlot()

• Fixed a typo that prevented labels to be bold in SCpubr::do_DimPlot() when cell borders are displayed.
• Added group.by and split.by functionality to SCpubr::do_DimPlot(). (#4)

SCpubr::do_DotPlot()

• Added ticks to axes.
• Modified default colors to convey a better aesthetic.

SCpubr::do_FeaturePlot()

• Fixed potential bugs in SCpubr::do_FeaturePlot when setting enforce_symmetry = TRUE.
• Changed default value of order in SCpubr::do_FeaturePlot() from TRUE to FALSE.
• Added min.cutoff and max.cutoff parameters to SCpubr::do_FeaturePlot(). This allows to effectively subset the color scale to the values provided. Cells outside the range will be converted to the min or max values provided, respectively. (#2)

SCpubr::do_GeyserPlot()

• Added flip parameter.

SCpubr::do_GroupwiseDEPlot()

• Fixed bug in SCpubr::do_GroupwiseDEPlot in which the heatmap could not be computed. (#3)
• Added extra checks to ensure proper input in SCpubr::do_GroupwiseDEPlot. (#3)

SCpubr::do_LigandReceptorPlot() (development release)

• Changed parameter x_labels_angle to rotate_x_axis_labels to keep a consistent terminology.

SCpubr::do_RidgePlot()

• Fixed a typo that made the lines in panel.grid.minor to be displayed in SCpubr::do_Ridgeplot().
• Added flip parameter.

SCpubr::do_ViolinPlot()

• Added split.by functionality to SCpubr::do_ViolinPlot(). (#4, #5)
• Added flip parameter.
• Now multiple features can be queried ad the same time. (#5)
• Changed feature parameter to features, to better reflect the multiple feature behavior.
• Recreated Seurat’s share.y.lims behavior and set it to share.y.lims parameter. (#5)

SCpubr v1.0.2-dev-stable

• Same as v1.0.2, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

SCpubr v1.0.1

• Rework on unit tests and examples so that it can pass CRAN R CMD Check without packages in Suggests. This is, to make sure all Suggested packages are used conditionally.

SCpubr v1.0.1-dev-stable

• Same as v1.0.1, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

SCpubr v1.0.0

• Modified internal checks so that the functions that do not use Seurat do not require this to be installed. This is just for the very side case in which somebody downloads the package just for the SCpubr::do_ColorPalette() function.
• Removed the option to use individual.titles, ’individual.subtitlesandindividual.captionsinSCpubr::do_NebulosaPlot()` as the benefit of such parameters did not surpass the problems the code was causing. The feature might come back in the future, once fully optimized.
• Removed SCpubr::save_Plot() function to align with CRAN policies that the package should not write to the file system. The code is still available in the v0.0.0.0.9000 release in Github.
• Removed SCpubr::do_LigandReceptorPlot(), SCpubr::do_SankeyPlot() and SCpubr::do_PseudotimePlot() to align with CRAN policies and make it possible to publish the package. These functions can still be accessed in the v0.0.0.0.9000 release in Github.
• Removed SCpubr::do_PseudotimePlot() for the reason above and because the dependency Matrix.utils was removed from CRAN on 09-10-2022.

SCpubr v1.0.0-dev-stable

• Same as v1.0.0, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

SCpubr 0.0.0.9000

• Added a NEWS.md file to track changes to the package.
• Prepare package for submission to CRAN.