NEWS.md

scCustomize 2.1.2 (2024-02-27)

Added

• None.

Changed

• None.

Fixes

• Fixed breaking bug (and CRAN check errors) in Plot_Density_Custom and Plot_Density_Joint_Only due to error in Nebulosa following ggplot2 v3.5.0 update. Functionality will be restored when Nebulosa package is updated.

scCustomize 2.1.1 (2024-02-23)

Added

• None.

Changed

• None.

Fixes

• Fixed breaking bug in as.liger that prevented function from running properly.

scCustomize 2.1.0 (2024-02-21)

Added

• Added title_prefix parameter to Iterate_DimPlot_bySample to unify with Meta_Highlight_Plot.
• Added function Split_Vector to split vector in chunks of predetermined sizes.
• Added new function Updated_HGNC_Symbols to update human gene symbols. After first use does not require internet connection.
• Added command logging to QC metric-related commands using Seurat::LogSeuratCommand().
• Added parameter plot_legend to plotFactors_scCustom to allow for removal to legend in factor loading plots.
• Added new functionality to Iterate_FeaturePlot_scCustom to allow for plotting multiple plots per page when saving to single PDF document (see new parameters: features_per_page and landscape.
• Added LIGER_Features utility function for LIGER objects (analogous to Seurat::Features()).
• Added new generic as.LIGER() as enhanced method for conversion of Seurat objects or lists of Seurat objects to single LIGER object.
• Added new generic as.anndata() to support conversion of Seurat and LIGER objects to anndata format.
• Added function Convert_Assay() to perform easy conversions of Seurat assays between V3/4 (Assay) and V5 (Assay5) formats.
• Added parameter assay_type to allow manual control of assay type when creating Seurat object from LIGER using Liger_to_Seurat. Now as.Seurat.
• Added param grid_color to Clustered_DotPlot to control the color of grid lines (default is no grid lines).
• Added ability to split identities in Clustered_DotPlot by additional variable and maintain expression information.
• Added Split_Layers() function for V5 objects.
• Added Add_Alt_Feature_ID to add alternative feature ids to an Assay5 meta.data slot.

Changed

• BREAKING CHANGES Several methods have been moved to S3 generics to function for both Seurat and LIGER objects using single function name and therefore some function names have changed. Old functions will give deprecation warning and direct users to new functions.
  • Add_Mito_Ribo() replaces Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER.
  • Add_Cell_Complexity() replaces Add_Cell_Complexity_Seurat and Add_Cell_Complexity_LIGER.
• BREAKING CHANGES Meta_Present_LIGER has been deprecated and wrapped inside of Meta_Present.
• SOFT-DEPRECATION The function Liger_to_Seurat() has been soft-deprecated. It is replaced by new extension of Seurat generic as.Seurat with added support for Liger objects, using all the same parameters as Liger_to_Seurat. Full deprecation will occur in v2.2.0.
• SOFT-DEPRECATION The function Gene_Present has been soft-deprecated. It is replaced by Feature_Present which functions identically but better reflects that features present may also be proteins. Full deprecation will occur in v2.2.0.
• Parameter legend in Iterate_DimPlot_bySample has been inverted to no_legend to match Meta_Highlight_Plot parameters.
• Updated Liger_to_Seurat() for compatibility with Seurat V5 structure (#153). Now part of as.Seurat.
• Default color palette change from v2.0.0 when number of groups is between 3-8 has been reverted. Polychrome palette is default when number of groups is between 3-36.
• In preparation of upcoming overhaul of rliger package, added package version checks to current rliger functions in order to prevent breaking errors. Next update v2.2.0 will add cross-functionality between rliger package versions (#161).

Fixes

• General typo and style fixes.
• Fixed point size check in some QC functions to avoid unnecessary error message.
• Fixed redundant warning messages in Stacked_VlnPlot due to rasterization defaults.
• Fixed issue setting alpha_na_exp appropriately in FeaturePlot_scCustom.
• Fixed issue setting alpha_exp between Seurat versions 4 and 5 (#144).
• Fix duplicate legends in DimPlot_scCustom when levels are missing from a split plot.
• Fixed bug in FeaturePlot_scCustom that could cause plots to be mislabeled when using split.by and depending on the order of features provided (#150).
• Fixes issue with automatic point size calculation for Seurat Objects.
• Added check for presence of dimensionality reduction in DimPlot_LIGER (#153).
• Fixed bug in Add_Mito_Ribo_LIGER that caused it to return value of 0 for all cells (Now part of renamed Add_Mito_Ribo S3 generic).
• Fixed legend display is Clustered_DotPlot to display percentage instead of proportion to match legend text.
• Fixed Percent_Expressing error when group_by = "ident".
• Fixed error that caused features in non-default assays to be returned as not found when attempting to plot.
• Fixed error in DotPlot_scCustom that didn't correctly pass group.by when plotting (#158).

scCustomize 2.0.1 (2023-11-17)

Added

• None.

Changed

• Removed warning in VariableFeaturePlot_scCustom now fixed in Seurat release.

Fixes

• Fixed error in Add_Mito_Ribo_Seurat causing failure due to error message when overwrite = TRUE.
• Fixed error in Add_Top_Gene_Pct_Seurat to avoid issue that accidentally could call function on normalized data.
• Fixed error in Add_Top_Gene_Pct_Seurat that caused error if more than one counts layer was present.
• Fixed error in QC_Histogram that prevented plotting or titling of plots.

scCustomize 2.0.0 (2023-11-13)

Added

• Added support for metrics produced by Cell Ranger multi pipeline to Read10X_Metrics via new parameter cellranger_multi.
• Added dot_size parameter to Seq_QC_Plot_* family of functions.
• Added two new sequencing QC functions to create and iterate barcode rank plots: Barcode_Plot and Iterate_Barcode_Rank_Plot.
• Added ident_legend parameter to QC_Plot_UMIvsGene to control show/hide of the identity legend (#121).
• Added support for sparse matrix input in CellBender_Feature_Diff.
• Added min_count_label in CellBender_Diff_Plot to better control feature labeling.
• Allow specification of meta data column containing sample names/IDs in Iterate_DimPlot_bySample using new sample_column parameter.
• Added new function MAD_Stats to calculate to the median absolute deviation of meta.data columns by grouping variable and across entire object.
• Added new function Add_Top_Gene_Pct_Seurat to add another QC measure of cell complexity to object meta.data. Returns percentage of counts occupied by top XX genes in each cell.
• Added ability to provide set of custom features to VariableFeaturePlot_scCustom using custom_features parameter.
• Added new overall cell QC metric function Add_Cell_QC_Metrics to simplify adding cell QC metrics. Single function call to add Mito/Ribo Percentages, Cell Complexity, Top Gene Percentages, MSigDB Percentages, IEG Percentages, and/or Cell Cycle Scoring (human only).
• Added 2 new gene lists to package data for use in Add_Cell_QC_Metrics function: "msigdb_qc_gene_list" and "ieg_gene_list".
• Added several internal functions to support new MsigDB and IEG capabilities of Add_Cell_QC_Metrics.
• Added new parameters plot_median and plot_boxplot to VlnPlot_scCustom (and VlnPlot_scCustom-based plots; e.g., QC_Plot_* family) for added visualization.
• Added QC_Histogram to plot QC features (or any feature) using simple histogram.
• Added FeatureScatter_scCustom function to customize Seurat's FeatureScatter plots.
• Added figure_plot parameter to all 2D DR (t-SNE, UMAP, etc) based plots (#127).

Changed

• Large scale under the hood code adjustments to ensure compatibility with Seurat V5 object structure.
• Internal code syntax updates independent of Seurat functionality.
• HARD DEPRECATION Split_FeatureScatter function has been completely deprecated and it's functionality has been moved to new FeatureScatter_scCustom.
• SOFT DEPRECATION The parameter gene_list in Iterate_FeaturePlot_scCustom and Iterate_VlnPlot_scCustom has been soft-deprecated and replaced by features parameter. Specifying gene_list will display deprecation warning but continue to function until next major update.
• The above soft deprecation was to clarify that other features besides genes can be plotted and coincides with update to functions to allow for iterative plots of meta.data or reductions in addition to assay features (#123).
• Internal rewrite of Read10X_Metrics to use new internal helper functions.
• Changed Liger_to_Seurat to transfer the liger_object@H slot in addition to H.norm slot already moved.
• Replaced length(x = colnames(x = obj) with length(x = Cells(x = obj) for accurate plotting based on V5 object structure.
• Gene_Present now accepts assay parameter.
• Internal reorganization of some functions within R/ for better organization.
• Updated default scCustomize color palettes (scCustomize_Palette). Now if number of colors is greater than 2 but less than 8 the default palette will be ColorBlind_Pal (previously it was "polychrome"). Polychrome remains the default when number of colors is between 9-36.
• Updated parameter default within scCustomize_Palette to ggplot_default_colors = FALSE to avoid uncessary error when no value supplied.
• Minimum version of scattermore package updated to v1.2.
• DimPlot_scCustom will now set label = TRUE if label.box is set to TRUE but label is not changed from default.
• Removed loading of full tidyverse in vignettes to remove from package suggests (lessen dependency installs when not completely needed).
• Replace Seurat PackageCheck (now deprecated), with rlang::is_installed() for non-dependency checks.
• Update vignettes with new features and bug fixes from old code.

Fixes

• Fixed issue in Read10X_Metrics that caused errors when reading files on windows operating system (#115).
• Fixed issue in Create_CellBender_Merged_Seurat when feature names are changed (underscore to dash) during object creation (#118).
• Fixed error in Read10X_h5_Mutli_Directory when reading Cell Ranger multi directories.
• Added new checks to VlnPlot_scCustom, DimPlot_scCustom, and DotPlot_scCustom to avoid otherwise ambiguous error messages (#120).
• Fixed internal check message accidentally user facing in VlnPlot_scCustom (#122).
• Fixed cli warning in Cell_Highlight_Plot that could cause function to error without proper error message.
• Fixed handling of file names in Read_* functions to avoid unnecessary errors.
• Replace superseded dplyr syntax/functionality drop_na(.data[[var]], with current dplyr syntax.
• Internal code fixes to accelerate plotting functions.
• Fixed default plot colors in VlnPlot-based plots when split.by is not NULL.
• Fixed error when trying to plot more than two variables with group.by when using DimPlot_scCustom (#128).
• Fixed errors in parameter description for Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER which incorrectly stated the names of new meta.data/cell.data columns to be added.
• Fixed bug in DotPlot_scCustom that prevented it from working unless group.by parameter was explicitly added.
• Fixed bug in Case_Check caused by typo.
• Fixed color warning messages in Cluster_Highlight_Plot and Meta_Highlight_Plot that were too verbose.
• Fixed bug in Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER which caused error when supplying custom list of features for non-default organism (#133).
• Fixed bug in DimPlot_scCustom preventing that errored when trying to split plot and use figure_plot at same time.

scCustomize 1.1.3 (2023-07-19)

Added

• None.

Changed

• None.

Fixes

• Fixed manual entry for Merge_Seurat_List.

scCustomize 1.1.2 (2023-07-18)

Added

• Added aspect_ratio parameter to all dimensionality reduction plots to control axes ratio of output plot.
• Added plot_median and median_size parameters to QC_Plots_* functions.
• Added split_collect parameter to FeaturePlot_scCustom to collect all guides when using split.by for a single feature (#94).
• Added new parameters to Clustered_DotPlot to allow modification of sizes of column text labels, legend text labels, and legend title labels (#96).
• Added new function Merge_Sparse_Multimodal_All for merging multi-modal data (1 matrix per modality) (#104).
• Added new parameter to Clustered_DotPlot named row_label_fontface to allow control of fontface used for row labels (#103).
• Added helper utility Reduction_Loading_Present, in part to fix issue with FeaturePlot_scCustom and internal feature checking.
• Added ability to turn off feature/ident clustering in Clustered_DotPlot using new parameters: cluster_feature, cluster_ident (#106).
• Added dot_size parameter to statistics plotting functions Plot_Cells_per_Sample and Plot_Median_* family.
• Added new parameter no_legend to Iterate_Meta_Highlight_Plot to allow for plotting with a plot title instead of plot legend (#108).

Changed

• Moved QC_Plots_Feature to use VlnPlot_scCustom under the hood like rest of QC_Plots_* functions.
• Renamed parameter abort in Meta_Present to return_none to align with Gene_Present and Reduction_Loading_Present.
• Replace superseded dplyr syntax/functionality summarise_at, select(.data[[var]]), and rename(.data[[var]]) with current dplyr syntax.
• Internal rewrite of plotting sections within Iterate_Cluster_Highlight_Plot and Iterate_Meta_Highlight_Plot to align with recent updates to base Cluster_Highlight_Plot and Meta_Highlight_Plot functions.

Fixes

• Fixed QC_Plots_Feature to respect parameters when passing to VlnPlot (#91).
• Fixed Read_CellBender_h5_* functions to support CellBender outputs from STARsolo- or Cell Ranger (pre-V3)-processed data (#99).
• Fixed FeaturePlot_scCustom to allow for plotting of dimensionality reduction loadings (#97).
• Fixed Read10X_Multi_Directory and Read10X_h5_Multi_Directory to support files processed with Cell Ranger multi pipeline.
• Fixed bug in Merge_Seurat_List that prevented add.cell.id from adding correct cell name prefixes (#113).

scCustomize 1.1.1 (2023-01-13)

Added

• Added label_color_num parameter to PalettePlot allow control of color labeling.
• Added ability to rotate x-axis of Stacked_VlnPlot 90 degrees or 45 (previously possible) (#84).
• Added error checks to Merge_Seurat_List to avoid ambiguous error messages on failure.
• Added Case_Check checks/messages to all feature-based plotting functions.

Changed

• BREAKING CHANGE Parameter in PalettePlot has been changed from palette to pal.
• Updated PalettePlot to support pal of class "colors".
• Moved viridis package to Suggests and use paletteer package for viridis palette shortcut functions.
• Fixed color palette continuity in Cluster_Highlight_Plot and Meta_Highlight_Plot.
• Fetch_Meta is now S3 generic function that can handle either Seurat or LIGER objects.
• Rearrange base R code within R/ scripts for better organization.
• Completed move of all scCustomize error/warning messages from base R to cli/rlang framework.
• Move feature checking to internal function.

Fixes

• Fixed potential for column name collision error in Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER.
• Fixed Add_Mito_Ribo_Seurat to respect provided mito_name, ribo_name and mito_ribo_name values.
• Updated out-dated documentation for number of package functions.
• Typo/styling fixes.

scCustomize 1.1.0 (2022-12-22)

Added

• Added merge parameter to Read10X_GEO, Read10X_h5_GEO, Read_GEO_Delim and Read_CellBender_h5_Multi_File.
• Added raster.dpi parameter to DimPlot_LIGER.
• Added label parameter to FeaturePlot_scCustom to avoid error collision (#80).
• Added vln_linewidth parameter to control violin outline line width (#32).
• Added quick meta data getter function Fetch_Meta for returning data.frame of object meta data.
• Added Extract_Sample_Meta to extract sample-level meta data from object.
• Added Cell_Highlight_Plot for highlight plots of custom cells not in active ident or meta data.
• Added flip parameter to Clustered_DotPlot to enable axes flipping (#69).

Changed

• Updated Imports/Suggests for CRAN compatibility.
• Under the hood code updates for CRAN compatibility.
• Rearrange base R code within R/ scripts for better organization.

Fixes

• Fixed missing documentation for number of package functions.
• Typo/styling fixes.

scCustomize 1.0.2 (2022-11-22)

Added

• None.

Changed

• Updated required Seurat version (v4.3.0) to avoid bug in FindMarkers.

Fixes

• None.

scCustomize 1.0.1 (2022-11-10)

Added

• Added CellBender_Feature_Diff to return data.frame with count sums and differences between raw and CellBender assays.
• Added CellBender_Diff_Plot to plot differences between raw and CellBender assays using data from CellBender_Feature_Diff.

Changed

• BREAKING CHANGE Function name changed, Add_CellBender_Diff is new name for Add_Cell_Bender_Diff in order to unify function names for CellBender related functions.
• Updated CellBender vignette with new functions.

Fixes

• Fixed for automatic color palette selection when only plotting one group.

scCustomize 1.0.0 (2022-10-25)

Added

• Added mito_name parameter to QC_Plots_Mito to allow for custom specification of meta data column name that contains mitochondrial information.
• Added QC_Plots_Combined_Vln() function to return patchwork layout of 3 QC plots.
• Added Rhesus Macaque (macaca mulatta) to the accepted species list for Add_Mito_Ribo_Seurat() and Add_Mito_Ribo_LIGER() (#28).
• Added alpha_exp and alpha_na_exp parameters to FeaturePlot_scCustom to allow for control of color scale transparency (#21).
• *_Highlight_Plot functions can now plot multiple variables simultaneously using either one color for all variables or one color per variable (#34).
• Added parameter figure_plot to DimPlot_scCustom(). This removes axes and axes labels and adds axis legend on left bottom corner of plot (#40).
• Added parameter plot_legend to Stacked_VlnPlot. This solves issue with returning only one shared legend across all features being plotted (#48).
• Added Add_Cell_Complexity_Seurat and Add_Cell_Complexity_LIGER functions to add cell QC complexity/novelty metric (log10(Genes) / log10(UMIs)).
• Added QC_Plots_Complexity plot for quick plotting of cell complexity score.
• Added 3 new CellBender functions Read_CellBender_h5_Mat, Read_CellBender_h5_Multi_Directory, Read_CellBender_h5_Multi_File to enable easy reading of new CellBender output files.
• Added raster.dpi parameter from Seurat to all DimPlot FeaturePlot or FeatureScatter based functions.
• Added add.noise parameter from Seurat to VlnPlot_scCustom Stacked_VlnPlot functions.
• Added group.by as default listed parameter to added to allVlnPlot based QC_Plot_*.
• Added ensembl_ids parameter for Add_Mito_Ribo_* functions. If ensembl_ids = TRUE functions will retrieve stored ensembl IDs representing mitochondrial and ribosomal genes for accepted default species.
• Added parameter label_feature_yaxis to FeaturePlot_scCustom. Allows for plotting of feature names on secondary y-axis when using split.by (#60).
• Added Add_Sample_Meta function for addition of sample-level meta data to cell-level @meta.data slot of Seurat objects.
• Added a matrix check in Read_GEO_Delim to check for issues with imported matrices. Check is modified version of SeuratObject::CheckMatrix called CheckMatrix_scCustom(). Will warn if infinite, logical, non-integer (whole), or NA/NaN values are detected in input matrix.
• QC_Plot_UMIvsGene will now returned filtered correlation value that takes into account meta_gradient_name if provided in addition to nFeature_RNA and nCount_RNA.
• Added new function Variable_Features_ALL_LIGER which allows for detection/selection of variable genes from entire LIGER object instead of iterating by dataset.
• Vignettes/Website updated with new function examples.

Changed

• DEPENDENCY CHANGE The required version of Seurat has been changed due to errors caused by updates to Matrix package and handling of sparse matrices. To avoid errors version requirement for Seurat has been updated to 4.2.0.
• DEPENDENCY CHANGE The dittoSeq package has been moved to Suggests to aid package installation. To catch errors a PackageCheck warning has been added where needed.
• BREAKING CHANGE Function name for iterative VlnPlot has been changed to Iterate_VlnPlot_scCustom to reflect that it now uses VlnPlot_scCustom to generate plots.
• QC_Plot_* functions now use VlnPlot_scCustom internally to unify color scheme and rasterization parameters.
• *_Highlight_Plot functions no longer display "Unselected" in plot legend and uses DimPlot_scCustom to generate plots (#34).
• Updated Marsh et al., 2022 citation in vignettes.
• Have begun to move information, warning, and error messages to rlang/cli framework for clarity and style.

Fixes

• Fixed DESCRIPTION file to specify colorway version upon installation (#25).
• Fixed bug preventing low_cutoff from plotting via QC_Plots_Mito.
• Fixed bug in Clustered_DotPlot that prevented setting identity colors (#29).
• Fixed bug in FeaturePlot_scCustom that returned NULL when setting combine = FALSE (#31).
• Fixed bug in Seq_QC_Plot_* functions which resulted in groups being plotted out of order when specifying plot_by parameter.
• Fixed bug in Seq_QC_Plot_* functions that created color palette error when color palettes were not being used.
• Fixed bug in DimPlot_scCustom that caused mismatch of colors between plots when using split.by if one of the plots was missing 1 or more of the group.by levels (#37).
• Fixed bug in VlnPlot_scCustom that caused raster warning messages to be displayed twice (#42).
• Fixed bug in Iterate_PC_Loading_Plots that caused error when specifying current directory with file_path = NULL or file_path = ""
• Fixed bug in DotPlot_scCustom that prevented plotting of features in meta.data slot (#44).
• Fixed error messaging/reporting in Stacked_VlnPlot when no supplied features were present.
• Fixed bug in plotFactors_scCustom that was ignoring provided file name.
• Fixed bug in plotFactors_scCustom that caused progress to only display progress up to 50% even when it was fully complete.
• Fixed bug in Clustered_DotPlot that resulted in error related to color palettes if number of clusters was greater than 36 (#49).
• Fixed bug in Add_Mito_Ribo_LIGER that resulted custom column names (e.g. mito_name = "pct.mt") being disregarded and also therefore issue with overwrite parameter. (#51).
• Fixed bug in Store_Misc_Info_Seurat that prevented function from working.
• Fixed bug in Plot_Density_Custom when supplying custom_palette and multiple features. (#51).
• Fixed bug in Clustered_DotPlot so that legend with identities is displayed by factor level of Seurat object idents (#55).
• Fixed bug in Split_FeatureScatter to remove test code that prevented function from working properly (#57).
• Fixed bug in DimPlot_All_Samples, Split_FeatureScatter, and DimPlot_scCustom that ignored factor order when plotting groups.
• Fixed error due to deprecation of functions in Matrix package v1.5-0+ (#61).
• Fixed error that prevent returning FeaturePlot_scCustom when setting split.by and one or more of features provided was not present in object (#64).
• Typo/styling fixes.

scCustomize 0.7.0 (2022-01-10)

Added

• Added VlnPlot_scCustom function.
• Added raster support to Stacked_VlnPlot
• Added make_unique parameter to Extract_Top_Markers function.
• Added Clustered_DotPlot function.
• Added Drosophila Melanogaster as default species option in Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER.

Changed

• Now requires Seurat v4.0.6 (instead of v4.0.5) to support ability to rasterize points in VlnPlot.
• viridis color palette shortcuts now contain palettes with 30 colors (increased from 10).

Fixes

• Fixed Read_Metrics_10X errors that occurred due to differing outputs depending on Cell Ranger version or type of assay.
• Added direct importFrom for DefaultDimReduc from SeuratObject package to avoid potential errors.
• Fixed typos/styling in function documentation.

scCustomize 0.6.3 (2021-12-16)

Fixes

• Fixed Read_Metrics_10X errors that occurred due to differing outputs depending on Cell Ranger version or type of assay.
• Added direct importFrom for DefaultDimReduc from SeuratObject to avoid potential errors.

scCustomize 0.6.2 (2021-12-01)

Fixes

• Fixed barcode name duplication checks in Merge_Sparse_Data_All. (#8)
• Fixed package imports in DESCRIPTION to avoid installation errors.
• Fixed NULL check in Read_Metrics_10X, Read10X_Multi_Directory, and Read10X_h5_Multi_Directory.

scCustomize 0.6.1 (2021-11-19)

Added

• Added plot spacing control to StackedVlnPlot with parameters plot_spacing and spacing_unit. (#6)
• Added scCustomize_Palette function select palette to use (simplify internal code).

Changes

• Changed citation info to reflect global DOI and not version DOI.

Fixes

• Restore package color palette defaults to Iterate_VlnPlot.
• Fix Iterate_... function checks for file path parameter if file_path = NULL.

scCustomize 0.6.0 (2021-11-16)

Added

• scCustomize is public!! Version 0.6.0 is released!

Changes

• Many function names have changed since private release see reference page/manual for updated function names.