1.1.0-dev-stable

Same as v1.1.0, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

devtools::install_github("enblacar/SCpubr", ref = "v1.1.0-dev-stable")

1.1.0

SCpubr v1.1.0

Can be installed via CRAN:

install.packages("SCpubr")

Or via GitHub:

devtools::install_github("enblacar/SCpubr", ref = "v1.1.0")

Patch notes

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.

1.0.4-dev-stable

Same as v1.0.4, but with all the functions that do not pass CRAN checks. These functions are: SCpubr::save_Plot() SCpubr::do_LigandReceptorPlot() and SCpubr::do_SankeyPlot().

devtools::install_github("enblacar/SCpubr", ref = "v1.0.4-dev-stable")

1.0.4

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.

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().

devtools::install_github("enblacar/SCpubr", ref = "v1.0.3-dev-stable")

1.0.3

Can be installed via CRAN:

install.packages("SCpubr")

Or via GitHub:

devtools::install_github("enblacar/SCpubr", ref = "v1.0.3")

SCpubr v1.0.3

General

• 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 accross 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.

1.0.2-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().

devtools::install_github("enblacar/SCpubr", ref = "v1.0.2-dev-stable")

1.0.2

Can be installed using:

devtools::install_github("enblacar/SCpubr", ref = "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)

1.0.1-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().

devtools::install_github("enblacar/SCpubr", ref = "v1.0.1-dev-stable")

1.0.1

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.

devtools::install_github("enblacar/SCpubr", ref = "v1.0.1")