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.