output_width and output_height to the Iterate_* family of plotting functions (#217).Random_Cells_Downsample that prevented setting identity using the group.by parameter.Cell_Highlight_Plot that didn't pass the reduction parameter properly (#216).return_plots in iterative plotting functions(#217).Major Updates to Functionality with rliger Package:
Added new utility functions to interact with liger v2.0.0+ object format change:
- Subset_LIGER to quickly subset by cluster or other meta data variable.
- Cells_by_Identities_LIGER to extract list of barcodes sorted by values within given meta data column.
Extended the following Seurat/SeuratObject generic functions to work seamlessly with liger objects:
- Cells to extract vector of all cells or list vectors of cells by dataset.
- Features to extract vector of all features or list vectors of features by dataset.
- WhichCells to extract vector or list of cells matching identity criteria.
- Embeddings to extract matrix containing dimensionality reduction embeddings or iNMF h.norm matrix.
- Idents and Idents<- to extract and set default identities/clusters.
Updated functions to interact with both old and new style liger objects:
- plotFactors_scCustom()
- Fetch_Meta
- Top_Genes_Factor
- Add_Mito_Ribo
- Add_Cell_Complexity
- DimPlot_LIGER
- Variable_Features_ALL_LIGER
- Feature_Present
New functions compatible with old and new style liger objects:
- Added new function Add_Hemo to add hemoglobin gene percentage for QC. Also added as parameter to Add_Cell_QC_Metrics. Add_Hemo supports all default species: (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and chicken) and works with both Seurat and liger objects.
New scCustomize generics to function across both Seurat and Liger objects:
- Add_Hemo (see above).
- Rename_Clusters now S3 generic for setting new active.ident (Seurat) or defaultCluster (Liger).
New functions for Seurat and rliger v2.0.0+ only:
- Added new function Find_Factor_Cor to return correlation matrix between factor gene loadings from liger or Seurat object.
- Added new function Factor_Cor_Plot to plot positive correlations from liger or Seurat object.
Updated functions to recommend new rliger equivalents for users with rliger v2.0.0+:
- as.LIGER
- as.Seurat
General scCustomize Updates:
New functions:
Add_Hemo to add hemoglobin gene percentage for QC. Also added as parameter to Add_Cell_QC_Metrics. Add_Hemo supports all default species: (human, mouse, marmoset, zebrafish, rat, drosophila, and rhesus macaque) and works with both Seurat and liger objects.seq_zeros() to create sequences with preceding zeros.Read_Metrics_CellBender to read in the summary metrics csv file produced by CellBender. Can either read all metrics files from parent directory of output folders or a single metrics file.Updated_MGI_Symbols to check for update gene names/symbols in mouse data (#202).Proportion_Plot to plot pie chart or bar chart of proportion (or total counts) of cells in each identity class.Random_Cells_Downsample to return either a vector or list with randomly downsampled cells for each identity class.Cells_per_Sample to quickly return data.frame with just number of cells per sample.Updated functions:
data_name and overwrite to Add_Alt_Feature_ID to support new storage location.cells parameter explicitly to FeatureScatter_scCustom.SpatialDimPlot_scCustom. Thanks for encouragement @puapinyoying @nina-hahn (#160).Read_Metrics_10X to read a single metrics csv file and return data formatted the same way as when reading multiple files.cutoff_line_width to the QC_Plot_* family of plots to control line thickness of cutoff lines.Cluster_Stats_All_Samples now returns data.frame with row order reflecting the frequency of cells.Add_Mito_Ribo now supports datasets aligned to multi-species reference genomes (#184).add_prop_plot to DimPlot_scCustom to return plot showing number or percent of cells per identity along with the DimPlot.colors_use_assay2 to FeaturePlot_DualAssay which allows for specification of different palettes for the two plots (#182).Add_Cell_QC_Metrics.Store_Misc_Info_Seurat and Store_Palette_Seurat.reduction parameter in Cluster_Highlight_Plot and Meta_Highlight_Plot (#198).show_row_names show_column_names, column_names_side, row_names_side, legend_position, legend_orientation, show_ident_legend, and show_ident_colors parameters to Clustered_DotPlot. Thanks for idea and code @johnminglu (#199).Split_Vector to allow user to specify number of chunks or size of chunks for splitting vector.RenameClusters with additional parameters to enable storage of both old idents and new idents in meta.data within the function.Add_Cell_QC_Metrics.Seurat to explicitly reveal list_species_names parameter.Add_Top_Gene_Pct_Seurat is now S3 generic that works with both Seurat and liger objects and has been renamed Add_Top_Gene_Pct.Add_Cell_QC_Metrics is now S3 generic and works with both Seurat and liger objects.Add_Alt_Feature_ID to @misc slot of object for safer storage across object filtering.as.anndata to explicitly check for installation of anndata before starting conversion (#162).Plot_Median_Genes, Plot_Median_UMIs, Plot_Median_Mito, Plot_Median_Other, Plot_Cells_per_Sample to understand "ident" as grouping variable.Store_Misc_Info_Seurat to use Seurat accessor/setter function Seurat::Misc().sample_names in Read_CellBender_h5_Multi_File to clarify parameter behavior (related to (#208)).Read_Metrics_10X to support adjusts to metrics summary format and metric names in output from Cell Ranger v9+.Plot_Density_Custom and Plot_Density_Joint_Only have been re-enabled for users with ggplot2 v3.5.0 following Nebulosa v1.12.1 update patch.Add_Cell_QC_Metrics when overwrite = TRUE (#165).DotPlot_scCustom (#158).as.anndata from Seurat conversion that previously caused failures (#168).Create_Cluster_Annotation_File if for file path and csv name errors.plot_median and more than one feature in VlnPlot_scCustom (#169).DimPlot_scCustom due to changes in guides updated with ggplot2 v3.5.0 (#171).Add_Sample_Meta that still errored when setting na_ok = TRUE.Plot_Median_* family that caused issues when group_by parameter was NULL.FeaturePlot_scCustom when setting combine = FALSE.DimPlot_scCustom that could cause blank plot when rasterizing points.MAD_Stats that didn't respect mad_num parameter (#183).MAD_Stats that could cause issues if mad_num was less than or equal to 0 and returned error if setting group_by_var to "ident".all_of/any_of syntax.Cluster_Highlight_Plot with split.by parameter (#201).Convert_Assay (#205).Updated_HGNC_Symbols due to change in URL path for gene names (#209).DimPlot_scCustom when split.by and label.box = TRUE.DiscretePalette_scCustom that didn't error when supplying invalid palette names.DimPlot_LIGER that provided uniformative error message when changing the default cluster ident.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.as.liger that prevented function from running properly.title_prefix parameter to Iterate_DimPlot_bySample to unify with Meta_Highlight_Plot.Split_Vector to split vector in chunks of predetermined sizes.Updated_HGNC_Symbols to update human gene symbols. After first use does not require internet connection.Seurat::LogSeuratCommand().plot_legend to plotFactors_scCustom to allow for removal to legend in factor loading plots.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.LIGER_Features utility function for LIGER objects (analogous to Seurat::Features()).as.LIGER() as enhanced method for conversion of Seurat objects or lists of Seurat objects to single LIGER object.as.anndata() to support conversion of Seurat and LIGER objects to anndata format.Convert_Assay() to perform easy conversions of Seurat assays between V3/4 (Assay) and V5 (Assay5) formats.assay_type to allow manual control of assay type when creating Seurat object from LIGER using Liger_to_Seurat. Now as.Seurat.grid_color to Clustered_DotPlot to control the color of grid lines (default is no grid lines).Clustered_DotPlot by additional variable and maintain expression information.Split_Layers() function for V5 objects.Add_Alt_Feature_ID to add alternative feature ids to an Assay5 meta.data slot.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.Meta_Present_LIGER has been deprecated and wrapped inside of Meta_Present.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.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.legend in Iterate_DimPlot_bySample has been inverted to no_legend to match Meta_Highlight_Plot parameters.Liger_to_Seurat() for compatibility with Seurat V5 structure (#153). Now part of as.Seurat.Stacked_VlnPlot due to rasterization defaults.alpha_na_exp appropriately in FeaturePlot_scCustom.alpha_exp between Seurat versions 4 and 5 (#144).DimPlot_scCustom when levels are missing from a split plot.FeaturePlot_scCustom that could cause plots to be mislabeled when using split.by and depending on the order of features provided (#150).DimPlot_LIGER (#153).Add_Mito_Ribo_LIGER that caused it to return value of 0 for all cells (Now part of renamed Add_Mito_Ribo S3 generic).Clustered_DotPlot to display percentage instead of proportion to match legend text.Percent_Expressing error when group_by = "ident".DotPlot_scCustom that didn't correctly pass group.by when plotting (#158).VariableFeaturePlot_scCustom now fixed in Seurat release.Add_Mito_Ribo_Seurat causing failure due to error message when overwrite = TRUE.Add_Top_Gene_Pct_Seurat to avoid issue that accidentally could call function on normalized data.Add_Top_Gene_Pct_Seurat that caused error if more than one counts layer was present.QC_Histogram that prevented plotting or titling of plots.multi pipeline to Read10X_Metrics via new parameter cellranger_multi.dot_size parameter to Seq_QC_Plot_* family of functions.Barcode_Plot and Iterate_Barcode_Rank_Plot.ident_legend parameter to QC_Plot_UMIvsGene to control show/hide of the identity legend (#121).CellBender_Feature_Diff.min_count_label in CellBender_Diff_Plot to better control feature labeling.Iterate_DimPlot_bySample using new sample_column parameter.MAD_Stats to calculate to the median absolute deviation of meta.data columns by grouping variable and across entire object.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.VariableFeaturePlot_scCustom using custom_features parameter.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).Add_Cell_QC_Metrics function: "msigdb_qc_gene_list" and "ieg_gene_list".Add_Cell_QC_Metrics.plot_median and plot_boxplot to VlnPlot_scCustom (and VlnPlot_scCustom-based plots; e.g., QC_Plot_* family) for added visualization.QC_Histogram to plot QC features (or any feature) using simple histogram.FeatureScatter_scCustom function to customize Seurat's FeatureScatter plots.figure_plot parameter to all 2D DR (t-SNE, UMAP, etc) based plots (#127).Split_FeatureScatter function has been completely deprecated and it's functionality has been moved to new FeatureScatter_scCustom.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.Read10X_Metrics to use new internal helper functions.Liger_to_Seurat to transfer the liger_object@H slot in addition to H.norm slot already moved.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.R/ for better organization.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.scCustomize_Palette to ggplot_default_colors = FALSE to avoid uncessary error when no value supplied.DimPlot_scCustom will now set label = TRUE if label.box is set to TRUE but label is not changed from default.PackageCheck (now deprecated), with rlang::is_installed() for non-dependency checks.Read10X_Metrics that caused errors when reading files on windows operating system (#115).Create_CellBender_Merged_Seurat when feature names are changed (underscore to dash) during object creation (#118).Read10X_h5_Mutli_Directory when reading Cell Ranger multi directories.VlnPlot_scCustom, DimPlot_scCustom, and DotPlot_scCustom to avoid otherwise ambiguous error messages (#120).VlnPlot_scCustom (#122).Cell_Highlight_Plot that could cause function to error without proper error message.Read_* functions to avoid unnecessary errors.drop_na(.data[[var]], with current dplyr syntax.VlnPlot-based plots when split.by is not NULL.group.by when using DimPlot_scCustom (#128).Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER which incorrectly stated the names of new meta.data/cell.data columns to be added.DotPlot_scCustom that prevented it from working unless group.by parameter was explicitly added.Case_Check caused by typo.Cluster_Highlight_Plot and Meta_Highlight_Plot that were too verbose.Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER which caused error when supplying custom list of features for non-default organism (#133).DimPlot_scCustom preventing that errored when trying to split plot and use figure_plot at same time.Merge_Seurat_List.aspect_ratio parameter to all dimensionality reduction plots to control axes ratio of output plot.plot_median and median_size parameters to QC_Plots_* functions.split_collect parameter to FeaturePlot_scCustom to collect all guides when using split.by for a single feature (#94).Clustered_DotPlot to allow modification of sizes of column text labels, legend text labels, and legend title labels (#96).Merge_Sparse_Multimodal_All for merging multi-modal data (1 matrix per modality) (#104).Clustered_DotPlot named row_label_fontface to allow control of fontface used for row labels (#103).Reduction_Loading_Present, in part to fix issue with FeaturePlot_scCustom and internal feature checking.Clustered_DotPlot using new parameters: cluster_feature, cluster_ident (#106).dot_size parameter to statistics plotting functions Plot_Cells_per_Sample and Plot_Median_* family.no_legend to Iterate_Meta_Highlight_Plot to allow for plotting with a plot title instead of plot legend (#108).QC_Plots_Feature to use VlnPlot_scCustom under the hood like rest of QC_Plots_* functions.abort in Meta_Present to return_none to align with Gene_Present and Reduction_Loading_Present.summarise_at, select(.data[[var]]), and rename(.data[[var]]) with current dplyr syntax.Iterate_Cluster_Highlight_Plot and Iterate_Meta_Highlight_Plot to align with recent updates to base Cluster_Highlight_Plot and Meta_Highlight_Plot functions.QC_Plots_Feature to respect parameters when passing to VlnPlot (#91).Read_CellBender_h5_* functions to support CellBender outputs from STARsolo- or Cell Ranger (pre-V3)-processed data (#99).FeaturePlot_scCustom to allow for plotting of dimensionality reduction loadings (#97).Read10X_Multi_Directory and Read10X_h5_Multi_Directory to support files processed with Cell Ranger multi pipeline.Merge_Seurat_List that prevented add.cell.id from adding correct cell name prefixes (#113).label_color_num parameter to PalettePlot allow control of color labeling.Stacked_VlnPlot 90 degrees or 45 (previously possible) (#84).Merge_Seurat_List to avoid ambiguous error messages on failure.Case_Check checks/messages to all feature-based plotting functions.PalettePlot has been changed from palette to pal.PalettePlot to support pal of class "colors".Cluster_Highlight_Plot and Meta_Highlight_Plot.Fetch_Meta is now S3 generic function that can handle either Seurat or LIGER objects.R/ scripts for better organization.Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER.Add_Mito_Ribo_Seurat to respect provided mito_name, ribo_name and mito_ribo_name values.merge parameter to Read10X_GEO, Read10X_h5_GEO, Read_GEO_Delim and Read_CellBender_h5_Multi_File.raster.dpi parameter to DimPlot_LIGER.label parameter to FeaturePlot_scCustom to avoid error collision (#80).vln_linewidth parameter to control violin outline line width (#32).Fetch_Meta for returning data.frame of object meta data.Extract_Sample_Meta to extract sample-level meta data from object.Cell_Highlight_Plot for highlight plots of custom cells not in active ident or meta data.flip parameter to Clustered_DotPlot to enable axes flipping (#69).R/ scripts for better organization.FindMarkers.CellBender_Feature_Diff to return data.frame with count sums and differences between raw and CellBender assays.CellBender_Diff_Plot to plot differences between raw and CellBender assays using data from CellBender_Feature_Diff.Add_CellBender_Diff is new name for Add_Cell_Bender_Diff in order to unify function names for CellBender related functions.mito_name parameter to QC_Plots_Mito to allow for custom specification of meta data column name that contains mitochondrial information.QC_Plots_Combined_Vln() function to return patchwork layout of 3 QC plots.Add_Mito_Ribo_Seurat() and Add_Mito_Ribo_LIGER() (#28).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).figure_plot to DimPlot_scCustom(). This removes axes and axes labels and adds axis legend on left bottom corner of plot (#40).plot_legend to Stacked_VlnPlot. This solves issue with returning only one shared legend across all features being plotted (#48).Add_Cell_Complexity_Seurat and Add_Cell_Complexity_LIGER functions to add cell QC complexity/novelty metric (log10(Genes) / log10(UMIs)).QC_Plots_Complexity plot for quick plotting of cell complexity score.Read_CellBender_h5_Mat, Read_CellBender_h5_Multi_Directory, Read_CellBender_h5_Multi_File to enable easy reading of new CellBender output files.raster.dpi parameter from Seurat to all DimPlot FeaturePlot or FeatureScatter based functions.add.noise parameter from Seurat to VlnPlot_scCustom Stacked_VlnPlot functions.group.by as default listed parameter to added to allVlnPlot based QC_Plot_*.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.label_feature_yaxis to FeaturePlot_scCustom. Allows for plotting of feature names on secondary y-axis when using split.by (#60).Add_Sample_Meta function for addition of sample-level meta data to cell-level @meta.data slot of Seurat objects.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.Variable_Features_ALL_LIGER which allows for detection/selection of variable genes from entire LIGER object instead of iterating by dataset.PackageCheck warning has been added where needed.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).low_cutoff from plotting via QC_Plots_Mito.Clustered_DotPlot that prevented setting identity colors (#29).FeaturePlot_scCustom that returned NULL when setting combine = FALSE (#31).Seq_QC_Plot_* functions which resulted in groups being plotted out of order when specifying plot_by parameter.Seq_QC_Plot_* functions that created color palette error when color palettes were not being used.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).VlnPlot_scCustom that caused raster warning messages to be displayed twice (#42).Iterate_PC_Loading_Plots that caused error when specifying current directory with file_path = NULL or file_path = ""DotPlot_scCustom that prevented plotting of features in meta.data slot (#44).Stacked_VlnPlot when no supplied features were present.plotFactors_scCustom that was ignoring provided file name.plotFactors_scCustom that caused progress to only display progress up to 50% even when it was fully complete.Clustered_DotPlot that resulted in error related to color palettes if number of clusters was greater than 36 (#49).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).Store_Misc_Info_Seurat that prevented function from working.Plot_Density_Custom when supplying custom_palette and multiple features. (#51).Clustered_DotPlot so that legend with identities is displayed by factor level of Seurat object idents (#55).Split_FeatureScatter to remove test code that prevented function from working properly (#57).DimPlot_All_Samples, Split_FeatureScatter, and DimPlot_scCustom that ignored factor order when plotting groups.FeaturePlot_scCustom when setting split.by and one or more of features provided was not present in object (#64).VlnPlot_scCustom function.Stacked_VlnPlotmake_unique parameter to Extract_Top_Markers function.Clustered_DotPlot function.Add_Mito_Ribo_Seurat and Add_Mito_Ribo_LIGER.VlnPlot.Read_Metrics_10X errors that occurred due to differing outputs depending on Cell Ranger version or type of assay.importFrom for DefaultDimReduc from SeuratObject package to avoid potential errors.Read_Metrics_10X errors that occurred due to differing outputs depending on Cell Ranger version or type of assay.importFrom for DefaultDimReduc from SeuratObject to avoid potential errors.Merge_Sparse_Data_All. (#8)Read_Metrics_10X, Read10X_Multi_Directory, and Read10X_h5_Multi_Directory.StackedVlnPlot with parameters plot_spacing and spacing_unit. (#6)scCustomize_Palette function select palette to use (simplify internal code).Iterate_VlnPlot.Iterate_... function checks for file path parameter if file_path = NULL.