NEWS.md

In SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

SCpbur v3.0.0 (In Development)

Reason for the mejor version change

• Due to the preparation for the publication of SCpubr's manuscript, a major effort has been made to further standardize and wrap up the package nicely.
• Some functions have been removed, and many have been renamed, for consistency.
• Development version of functions have been transferred to the normal release, with the exception of SCpubr::do_SavePlot().

General

• Enhanced startup message for clarity. Not it guides the user to run SCpubr::package_report(extended = TRUE) to get an overview of the missing dependencies.
• Added black border to glyphs in legends.
• Whenever a categorical color scale is used, now you can set colorblind = TRUE, and it will pull from a collection of different published colorblind-safe palettes. If the length of the classes in the categorical variable matches the length of one of the palettes, that palettes is used. If not, a pool will be selected, with a total maximum of 85 categories allowed. If colors.use is used, colorblind has no effect (thus, check if your palette is colorblind-safe with do_ColorBlindCheck()). For continuous variables, YlGnBu is used. For divergent variables, RdBu is used. Both YlGnBu and RdBu are colorblind-safe. Since they are set as default, there is no need for colorblind parameter in the functions that only plot continuous/divergent variables.
• Added support to show the values as text in most heatmap-based functions. This is achieved by using values.show = TRUE.
• Aesthetics of the text labels can be tuned with values.threshold, values.size and values.round.
• Fixed an issue where symmetry_center would not work as intended. Now it correctly displays the color scale with the provided value in the center.

Added functions

• do_WafflePlot(): This function displays proportions as a pictogram grid of 10x10 tiles. It helps to visually see at a glance the proportions of your data. This fails to correctly convey decimal proportions and completely ignores heavily under-represented classes in your dataset.
• do_RankedExpressionHeatmap() to plot expression values as a heatmap along a dimensional reduction component.
• do_ColorBlindCheck to provide a comparative view of a given color paletter under different kinds of color blindness. This will allow to check for the suitability of a given set of colors for publication.

Removed functions

• do_FunctionalAnnotationPlot().
• do_GroupedGOTermPlot().

The reason behind it is that they, together with do_TermEnrichmentPlot() targeted the same analysis and, therefore, were redundant.

Renamed functions

In an effort to standardize function names, the following changes have been implemented:

• do_DiffusionMapPlot() is now called do_RankedEnrichmentHeatmap().
• save_plot() (development release only) is now called do_SavePlot().
• package_report() is now called do_PackageReport().
• do_LoadingsPlot() is now called do_LoadingsHeatmap().
• do_AffinityAnalysisPlot() is now called do_ActivityHeatmap().
• do_PathwayActivityPlot() is now called do_PathwayActivityHeatmap().
• do_TFActivityPlot() is now called do_TFActivityHeatmap().
• do_GroupwiseDEPlot() is now called do_GroupwiseDEHeatmap().
• do_CopyNumberVariantPlot() is now called do_CNVHeatmap().
• do_CorrelationPlot() is now called do_CorrelationHeatmap().
• do_MetadataPlot() is now called do_MetadataHeatmap().
• do_GeyserPlot() is now called do_StripPlot().

Heavily modified functions.

• do_TermEnrichmentPlot(): Recoded the whole function. Now accepts the result of using clusterProfiler::enrichGO(), clusterProfiler::enrichKEGG(), etc. The output is a dot plot with the terms on the Y axis, the Gene Ratio in the X, colored by the adjusted p-value and size mapped to the Gene Count.
• do_DotPlot(): Removed dependencies with Seurat::DotPlot().
• do_RankedEnrichmentPlot(), do_EnrichmentHeatmap() and do_SCEnrichmentHeatmap() do not longer accept flavor = "AUCell" due to dependency issues and lack of development support.

The reason of these modification is to allow for a much clearer and concise output than before.

do_ActivityHeatmap()

• Changed legend title to "Z-Scored | ulm score", for consistency with other functions in the package.

do_AlluvialPlot()

• Enforced a minimum version of ggalluvial to deal with deprecation of functions from dplyr and tidyr that were still used in ggalluvial functions.
• Modified the legend items to have a black border.
• Changed default legend position to bottom and legend title to top and centered.

do_BoxPlot()

• Added legend.ncol, legend.nrow and legend.byrow parameters to control legend behavior.
• Fixed a bug in which map_signif_levels would only accept a logical and not custom mappings.
• When map_signif_levels is used, the mapping now appears as a plot legend for clarity.
• Added black borders to the legend glyphs when using use_silhouette = FALSE.

do_CellularStatesPlot()

• Added reference lines to the plot to better visualize the segments.
• Added black border around the legend items.
• Fixed bug where axis text will always display in bold.

do_ChortDiagramPlot()

• Added font.size parameter to control the font size of the plot.

do_CNVHeatmap()

• Added include_chr_arms parameter to decide whether the heatmap should include a breakdown of the arms or just keep it by chromosomes.

do_ColorPalette()

• Changed "Wheel" to "Color wheel" when plotting the output without additional parameters.

do_DimPlot()

• Fixed a bug caused by using cells.highlight with only one cell.
• Fixed a bug causing the "Combined" plot resulting of the use of split.by and group.by to have a different size than the rest of panels when ncol parameter was also used.
• Fixed a bug causing a "selected_cells" plot title to show up when using cells.highlight and idents.highlight.
• Changed the plot title of the "Combined" plot to either group.by or split.by depending of the usage context.
• Added split.by.combined parameter and set its default value to TRUE. This allows to toggle on or off whether to display the combined view when split.by is used.
• However, when split.byis used alongside group.by, it is now enforced to show the combined plot (split.by.combined = TRUE), to avoid bugs.
• Added legend.dot.border parameter to select whether we want a black border around the legend dots or not.
• Fixed a bug in which font.family would not be applied when label = TRUE.
• Fixed a bug in which groups would not cluster if cluster = TRUE if there were missing values.

do_DotPlot()

• Fixed a bug that caused sequential palettes to not be checked properly.
• Changed default value of dot.scale to 8.
• Removed legacy parameter colors.use, which had no effect as of previous version but was still listed as parameter.
• Removed dependency with Seurat::DotPlot(). This means that there will be some differences with the output of this function. However, this is a design choice for the sake of preventing future dependency problems.
• Added split.by parameter.
• If features is provided as a named list, the plot facets them based on the belonging list (duplcated genes are removed). Cannot be used alongside split.by.
• Removed scaleand scale.by parameters. In the sense of how they worked in Seurat.
• Added zscore.data parameter. When set to TRUE, it computes Z-scores for each gene across the different groups, allowing for inspection of which group has highest or lowest expression, but prevents you from comparing values across different genes. It is intended to be used alongside slot = "data".
• Removed the possibility to use a list of features. Instead, facets are being drawn according to split.by parameter.
• Removed dot_border. This is a design choice of SCpubr.
• Added dot.min parameter to exclude dots falling below a threshold for P.Exp.

do_EnrichmentHeatmap()

• Changed default value of scale_scores to FALSE.
• Fixed a bug in which scores were not actually being scaled when scale_scores = TRUE.
• Fixed a bug in which setting scale_scores = TRUE and features.order would trigger an error since the output had the suffix _scaled on it. This has been patched.

do_FeaturePlot()

• Fixed a bug in which legend titles would not show up as intended.
• Enabled the use of several legend titles when multiple features are provided. The number of legend titles and features have to be equal.
• Fixed a bug in which font.family would not be applied when label = TRUE.
• Added scale.limits parameter to control the range of values the color scale should take. This is specially useful if you want to plot several features and make the color comparable between them.

do_GroupwiseDEHeatmap()

• Reduced the legend title texts to allow for more room in the plot.
• Fixed a bug in which providing a DE genes object with p_val_adj = 0 would cause the function to crash.

do_LigandReceptorPlot()

• Added a new parameter top_interactions_by_group which when set to TRUE will report for each pair of source and target, as many interactions as stated in top_interactions.

do_MetadataHeatmap()

• Modified the legend items to have a black border.
• Set cluster = FALSE as default.

do_PathwayActivityHeatmap

• Changed legend title to "Z-Scored | score", for consistency with other functions in the package.

do_RidgePlot()

• Removed size = 1.25 aesthetic from the call to ggridges::geom_ridge....
• Set default legend position to bottom.
• Fixed a bug in which plot grid would not react properly to flip.
• Simplified the functionality of the function due to inconsistent interactions with ggridges package. As such, parameters compute_quantiles, compute_custom_quantiles, quantiles, compute_distribution_tails, prob_tails and color_by_probabilities are removed.

do_SavePlot()

• Added limitsize parameter, that allows for very big ggplot2-based plots to be saved with big dimensions.

do_TFActivityHeatmap()

• Changed legend title to "Z-Scored | score", for consistency with other functions in the package.

do_ViolinPlot()

• Added order parameter to reorder the groups based on the median. Only works when split.by is set to NULL.
• Fixed typos in error logging.
• Fixed a bug in which color palettes would not display by default when using split.by.

do_VolcanoPlot()

• Fixed an issue in which tags would be duplicated when using use_labels = TRUE in combination with order_tabs_by = "both".
• Renewed aesthetics.
• Parameter colors.use now defaults to NULL, allowing a default color scheme to take place. Setting this parameter to a color will modify the color scheme appropriately.
• Simplified axis titles.

SCpbur v2.0.2

General.

• Fixed a bug that prevented error messages stating the dependencies missing per function to show up properly.
• Fixed assumptions on Seurat v4 and v5 and reverted to the use of cannonical GetAssayData and SetAssayData functions.
• Fixed dependency problems with archived packages.

do_BeeSwarmPlot()

• Changed default continuous palette to YlGnBu.
• Changed default legend title to feature_to_rank if continous_feature = TRUE.
• Changed default value of sequential.direction to 1.
• Changed default value of legend.position to bottom when continuous_feature = FALSE.

do_BoxPlot()

• Changed default value of legend.position to bottom.
• Fixed a bug in which legend key glyphs would not show up when using use_silhouette = TRUE.

do_CopyNumberVariantPlot()

• Fixed an issue in which using min.cutoff or max.cutoff would render the values outside these bounds to NA and therefore being plotted as grey. Now they will have the highest/lowest value possible.

do_FeaturePlot()

• Added symmetry.type parameter, that allows to control how the symmetry is computed: either in absolute values (taking into account the highest and lowest value) or in the middle point specified by symmetry.center.
• Added symmetry.center parameter, that allows to control the center of symmetry when symmetry.type is set to centered.

do_ViolinPlot()

• Changed default value of legend.position to bottom.
• Fixed a bug in which the default color palette would not be applied when plot_boxplots = FALSE.
• Added legend.title.position parameter and set it up as top by default.
• Fixed a bug in which plot grid would not react properly to flip.

SCpubr v2.0.1

General

• Refactored startup messages to comply with CRAN policies.

Removed functions

• Removed SCpubr::check_dependencies() to support the use of SCpubr::package_report().

SCpubr::do_EnrichmentHeatmap

• Fixed a bug that checked the package dependencies for the wrong function.

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

• Changed viridis_color_map to viridis.palette.
• Changed viridis_direction to viridis.direction.
• Changed sequential_direction to sequential.direction.
• Changed rotate_x_axis_labels to axis.text.x.angle.
• Changed rotate_strip_text to strip.text.angle.

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

• SCpubr::do_MetadataPlot() to generate metadata heatmaps with ease both from Seurat object or from a data frame. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::do_SCExpressionHeatmap() to generate heatmaps of expression of genes across all cells in the dataset. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::do_SCEnrichementHeatmap() to generate heatmaps of enrichment of genes across all cells in the dataset. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::do_AffinityAnalysisPlot() to assess the affinity of gene sets to subset of cells in the Seurat objects using the weighted means algorithms from DecoupleR. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::do_LoadingsPlot() to generate a summary heatmap of the PCA loadings (top and bottom scored genes for each PC) together with a expression heatmap of the same genes. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::do_DiffusionMapPlot() to analyze the output of a diffusion map analysis on the context of enrichment in gene sets used for the generation of the diffusion map. Will be first released as part of the development version and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
• SCpubr::check_dependencies() to generate a per-function summary of the needed packages to run the function. The report has been enhanced with cli package and now clearly illustrates what is missing to run the function.

Removed functions

• SCpubr::do_SankeyPlot() has been removed and replaced by SCpubr::do_AlluvialPlot(), which is present in the official CRAN versions.
• SCpubr::do_PseudotimePlot() has been removed indefinitely until a better, revamped, state-of-the-art version is generated.
• SCpubr::do_AzimuthAnalysisPlot() has been removed as the output can be accomplished by a combination of the current functions in SCpubr. A vignette will be added to reproduce the same analysis.

General

• Now when using min.cutoff or max.cutoff, the legend will show that the min/max value is higher/lower than the one provided, if such value appeared originally in the legend breaks. This potentially interacts with enforce_symmetry.
• Added number.breaks parameter to control the number of breaks in the legend of ggplot2-based plots. It will not always work, as the function will try to fit the breaks accordingly. But still, will give some range of freedom to the user.
• Removed colorsteps from legend.type parameters as it was prone to generate unintended bugs.
• Changed default values from min.cutoff and max.cutoff from NULL to NA.
• Implemented diverging.palette parameter in all plots that have a symmetrical color scale to help selecting other possible color scales for the plot.
• Implemented sequential.palette parameter in all plots that have a continuous, non-symmetrical color scale to help selecting other possible color scales for the plot, in the case the user does not want to use viridis color scales.
• Renamed SCpubr::state_dependencies() to SCpubr::check_dependencies().
• Renewed printed messages at startup and while running functions using cli package.
• Added the complete control of the font style of plot titles, subtitles, captions, axis titles, axis text, legend titles and legend text. For this, the following parameters have been added to all ggplot2-based functions:
  • plot.title.face: To control the style of the title.
  • plot.subtitle.face: To control the style of the subtitle.
  • plot.caption.face: To control the style of the caption.
  • axis.title.face: To control the style of the axis title.
  • axis.text.face: To control the style of the axis text.
  • legend.title.face: To control the style of the legend title.
  • legend.text.face: To control the style of the legend text.
• Changed default font style for legend text from bold to plain.
• Changed default font style for axis text from bold to plain.
• When using plot.axes = TRUE parameter in SCpubr::do_DimPlot(), SCpubr::do_FeaturePlot() and SCpubr::do_NebulosaPlot(), now the entirety of the X and Y axis is removed, titles included.
• Remove plot margin padding in SCpubr::do_DimPlot(), SCpubr::do_FeaturePlot() and SCpubr::do_NebulosaPlot().

SCpubr::do_AlluvialPlot

• Added sequential.palette and sequential.direction parameters.

SCpubr::do_BarPlot

• Added facet.by parameter to extra group the bars by a third metadata variable.
• Added order.by to reorder the bars when using position = fill based on a value in group.by.
• Limited the possible interactions from group.by, split.by and order.by to those that make sense to plot. For instance, a bar plot using group.by and position = fill but not using split.by resulted in bars of equal lenght with only one value per group of proportion 1.
• Set default value of plot.grid to FALSE.
• Added parameter add.n to display the total count on top when position = fill.
• Added parameter add.n.face to control the appearance of the text displayed.
• Added parameter add.n.expand to control the range of values in the Y axis. This has to be minimum 0 and maximum at least 1. This is set in order to tweak the limits so that the labels fit when flip = TRUE.

SCpubr::do_BeeSwarmPlot

• Added order parameter to reorder the groups based on the median rank.

SCpubr::do_BoxPlot

• Changed the reordering of boxplots based on the median rather than the mean.
• Added na.rm to geom_boxplot to avoid unnecessary warnings when introducing NAs as part of the data.
• Fixed a bug in which order would not work if NAs are in the data.
• Changed default value of boxplot.linewidth from 1 to 0.5.
• Fixed a bug in which when using a combination of group.by and split.by, the package would check that the colors provided to colors.use need to match the values in group.by and not split.by.

SCpubr::do_CorrelationPlot

• Added parameter to fix a bug in which viridis scales did not apply due to the lack of the parameter.
• Added min.cutoff and max.cutoff parameter to add cutoffs to the scales.
• Added mode = "jaccard" to compute a correlation matrix of a list of gene sets based on jaccard similarity.
• Added use_viridis, sequential.palette and sequential_direction and diverging.palette to control color palettes.
• Added cluster parameter to toggle on/off the clustering of the rows and columns in the heatmap.
• Added remove.diagonal parameter to toggle on/off the conversion of the diagonal in the correlation matrix to NA.
• Fixed several issues with setting cutoffs for the color scale using min.cutoff and max.cutoff.
• Fixed an issue where number.breaks will not work in mode = "jaccard".

SCpubr::do_CopyNumberVariantPlot()

• Removed the option to compute Feature and Geyser plots.
• Instead, a new paramerter return_object has been added to return the Seurat object with a new assay containing the CNV scores per cell on the data slot of the CNV_scores assay.
• The main output visualization is now a heatmap with the averaged scores by chromosome and groups and also by chromosome arms.

SCpubr::do_DimPlot

• Modified underlying code to correctly display borders around cells when cells.highlight or idents.hightlight or idents.keep are used. Also removed the "Not selected" item from the legend when doing so, as it was redundant.
• Fixed a bug in which multiple legend would appear when using a combination of group.by and split.by, given that the individual UMAPs would not have the same number of entities to plot and color.

SCpubr::do_DotPlot

• Added scale parameter to allow for the data to be scaled or not scaled.
• Removed split.by parameter in favor or the higher consistency and proper functionality accross parameters. Will probably come in the future, implemented outside of the umbrella of Seurat.
• Renamed parameter cluster.idents to cluster.
• Removed the limitation of flip when features was a list of genes. Now any combination of flip and features is possible.

SCpubr::do_EnrichmentHeatmap

• Removed options to plot FeaturePlots, GeyserPlots, ViolinPlots, etc. - together with its related parameters. For the sake of simplicity in the function and its use, the user can get the Seurat object back with return_object = TRUE and plot the enrichment scores separately, that are stored as a new Assay.
• Removed return_matrix parameter as the scores can now be retrieved from the Seurat object as an assay.
• Enforcing the use of named lists as input for the function.
• Added cluster parameter to allow for clustering of rows and columns.
• Added groups.order to allow for specifically arrange the groups defined by group.by with a given order.
• Added features.order to allow for specifically arrange the gene sets defined by input_gene_list.

SCpubr::do_ExpressionHeatmap

• Added cluster parameter to allow for clustering of rows and columns.
• Added groups.order to allow for specifically arrange the groups defined by group.by with a given order.
• Added features.order to allow for specifically arrange the features defined by features.

SCpubr::do_FeaturePlot

• Modified underlying code to show a border around selected cells when using split.by, cells.hightlight and idents.highlight.
• Added parameter border.density to reduce the amount of extra cells drawn on the background to generate the borders. This will be a number between 0 and 1 corresponding to the quantile of the distribution of density of the points in the scatterplot drawn in the background. The lower the value, the harder it will be to keep a border around all cells, while it will significantly reduce the overall weight of the plot object.
• Added parameter group.by, that allows to plot a big dot in the center of each group designated by group.by and thus allowing to locate easily where each identity is in the FeaturePlot. Also, plots a legend matching the color of the dots. This can be tweaked with additional parameters such as:
• group.by.show.dots to controlw hether these dots are plotted or not (to allow only plotting colored borders around cells - see below).
• group.by.dot.size to control the size of the introduced dots.
• group.by.cell_border to plot another contour-like border which also displays the color coding of the clusters designated by group.by, to signal the reach of each cluster. However, this basically signals the cluster the cells in the periphery of the cell blobs belong to. Take that into account.
• group.by.cell_borders.alpha controls the alpha of the new cell borders.
• group.by.legend controls the legend title of the new legend.
• Renamed split.by.idents to idents.keep to better synergize with the parameter in SCpubr::do_DimPlot. Only works when split.by is used.

SCpubr::do_FunctionalAnnotationPlot

• Removed the tree plots as they proved to behave inconsistently across datasets and the quality of visualizations were compromised.
• Removed the option to plot the bar plots and dot plots in the sake of a more simplified, streamlined plot generation.
• The option to return the result matrix using return_matrix is added, so that the user can use it to compute further analysis or visualizations.

SCpubr::do_FunctionalAnnotationPlot

• Renamed order_by_mean to order.
• Ordering using order = TRUE now is done based on the median instead of the mean.

SCpubr::do_LigandReceptorPlot()

• Modified the accepted input so that only the result of liana::liana_aggregate() is taken into account.
• Removed arrange_interactions_by as now the function only accepts the output of liana::liana_aggregate().
• Added a sort.by parameter instead to select how the output of liana::liana_aggregate() should be ordered prior the subset by top_interactions. Five modes are available:
  • A: Orders the output by specificity.
  • B: Orders the output by magnitude.
  • C: Orders the output by specificity then magnitude. This prioritizes the specificity column.
  • D: Orders the output by magnitude then specificity. This prioritizes the magnitude column.
  • E: Orders the output by specificity and magnitude providing equal weights to both columns.
• Removed flip parameter as the output was prone to errors.
• Removed parameter compute_ChordDiagrams and added return_interactions. This parameter returns two tibbles that can be used alongside SCpubr::do_ChordDiagramPlot to plot the diagrams.
• Now the filtering applied by using keep_source and keep_target takes place before subsetting for the top N interactions defined by top_interactions. This ensures that, if the user wants to focus on a given interaction subset, we retrieve the most important interactions for the subset.
• Added magnitude and specificity columns to allow the user to choose which variables to use for plotting.
• Added sorting.type.magnitude and sorting.type.specificity to allow the user to choose how the columns are sorted prior plotting.
• Added invert_magnitude and invert_specificity to allow the user to choose how the data is displayed for columns that tend to 0. Inverting performs a -log10 transformation on the column.
• Added a verbose parameter and set it to TRUE by default to inform the user of the arrangements taking place in the output of liana::liana_aggregate() prior plotting.

SCpubr::do_PathwayActivityPlot()

• Removed the option to plot geyser and feature plots to simplify the use (and computational time) of the function.
• Introduced return_object parameter that returns the Seurat object with the new assay to use for other plotting purposes (such as Geyser and Feature plots).
• Removed options to plot FeaturePlots, GeyserPlots - together with its related parameters. For the sake of simplicity in the function and its use, the user can get the Seurat object back with return_object = TRUE and plot the scores separately.
• Added slot parameter to decide whether to plot scale data or not.
• Fixed bug in which after setting enforce_symmetry = FALSE the color palette used was diverging.palette instead.

SCpubr::do_TFActivityPlot()

• Removed the option to plot geyser and feature plots to simplify the use (and computational time) of the function.
• Introduced return_object parameter that returns the Seurat object with the new assay to use for other plotting purposes (such as Geyser and Feature plots).
• Removed options to plot FeaturePlots, GeyserPlots - together with its related parameters. For the sake of simplicity in the function and its use, the user can get the Seurat object back with return_object = TRUE and plot the scores separately.
• Added slot parameter to decide whether to plot scale data or not.
• Fixed bug in which after setting enforce_symmetry = FALSE the color palette used was diverging.palette instead.

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.

SCpubr documentation built on Aug. 21, 2025, 6 p.m.