v2.0.2-dev-stable

Same as v2.0.2, but with all the functions that do not pass CRAN checks and those that are in active development.

On top of that, also contains these changes that will roll out on version 2.0.3:

do_DimPlot()

• Fixed a bug caused by using cells.highlight with only one cell.

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_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.

Can be installed using:

devtools::install_github("enblacar/SCpubr", ref = "v2.0.2-dev-stable")

2.0.2

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.

2.0.1-dev-stable

Same as v2.0.1, but with all the functions that do not pass CRAN checks and those that are in active development.

Can be installed using:

devtools::install_github("enblacar/SCpubr", ref = "v2.0.1-dev-stable")

2.0.1

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.

2.0.0-dev-stable

Same as v2.0.0, but with all the functions that do not pass CRAN checks and those that are in active development.

Can be installed using:

devtools::install_github("enblacar/SCpubr", ref = "v2.0.0-dev-stable")

2.0.0

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 facet.by.direction parameter to decide in which direction the facets are drawn.
• 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 bor...

1.1.2-dev-stable

Same as v1.1.2, 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 = "v1.1.2-dev-stable")

1.1.2

Hotfixes in unit tests to comply with CRAN checks.

Can be installed via CRAN:

install.packages("SCpubr")

Or via GitHub:

devtools::install_github("enblacar/SCpubr", ref = "v1.1.2")

1.1.1-dev-stable

Same as v1.1.1, 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 = "v1.1.1-dev-stable")

1.1.1

Hotfixes in unit tests to comply with CRAN checks.

Can be installed via CRAN:

install.packages("SCpubr")

Or via GitHub:

devtools::install_github("enblacar/SCpubr", ref = "v1.1.1")