scCustomize 3.0.0 (2024-12-05)

Added

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:
- 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, and rhesus macaque) and works with both Seurat and liger objects.
- Added new function seq_zeros() to create sequences with preceding zeros.
- Added new function 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.
- Added Updated_MGI_Symbols to check for update gene names/symbols in mouse data (#202).
- Added plotting function Proportion_Plot to plot pie chart or bar chart of proportion (or total counts) of cells in each identity class.
- Added new function Random_Cells_Downsample to return either a vector or list with randomly downsampled cells for each identity class.
- Added new function Cells_per_Sample to quickly return data.frame with just number of cells per sample.

Updated functions:
- Added new parameters data_name and overwrite to Add_Alt_Feature_ID to support new storage location.
- Added cells parameter explicitly to FeatureScatter_scCustom.
- Added Chicken (Gallus gallus) to default species for QC functions. Thanks @dpearton; (#176).
- Added new plotting function SpatialDimPlot_scCustom. Thanks for encouragement @puapinyoying @nina-hahn (#160).
- Added ability of Read_Metrics_10X to read a single metrics csv file and return data formatted the same way as when reading multiple files.
- Added parameter 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).
- Added parameter add_prop_plot to DimPlot_scCustom to return plot showing number or percent of cells per identity along with the DimPlot.
- Added optional parameter colors_use_assay2 to FeaturePlot_DualAssay which allows for specification of different palettes for the two plots (#182).
- Added new folder and scripts (see “data-raw/” on GitHub) detailing the creation of gene lists used in Add_Cell_QC_Metrics.
- Added ensembl ID support for percent hemoglobin, msigdb, and IEG gene sets (#186).
- Add verbosity parameter to Store_Misc_Info_Seurat and Store_Palette_Seurat.
- Explicitly reveal the reduction parameter in Cluster_Highlight_Plot and Meta_Highlight_Plot (#198).
- Added 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).
- Updated Split_Vector to allow user to specify number of chunks or size of chunks for splitting vector.
- Update RenameClusters with additional parameters to enable storage of both old idents and new idents in meta.data within the function.
- Update Add_Cell_QC_Metrics.Seurat to explicitly reveal list_species_names parameter.
- Added new vignette for spatial plotting.
- Added new and expanded vignette on use of object QC functions for better clarity on these functions and their uses (previously was part of QC Plotting & Helpers/Utilities Vignettes). Plotting elements of QC Plotting vignette are unchanged.

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scCustomize 2.1.2 (2024-02-27)

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scCustomize 2.1.1 (2024-02-23)

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scCustomize 2.1.0 (2024-02-21)

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scCustomize 2.0.1 (2023-11-17)

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scCustomize 2.0.0 (2023-11-13)

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scCustomize 1.1.3 (2023-07-19)

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scCustomize 1.1.2 (2023-07-18)

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scCustomize 1.1.1 (2023-01-13)

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scCustomize 1.1.0 (2022-12-22)

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scCustomize 1.0.2 (2022-11-22)

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scCustomize 1.0.1 (2022-11-10)

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scCustomize 1.0.0 (2022-10-25)

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scCustomize 0.7.0 (2022-01-10)

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scCustomize 0.6.3 (2021-12-16)

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scCustomize 0.6.2 (2021-12-01)

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scCustomize 0.6.1 (2021-11-19)

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scCustomize 0.6.0 (2021-11-16)

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