Changelog

Source: NEWS.md

scop 0.6.0

• func:
  • PrepareEnv(): Enhanced with environment caching mechanism to avoid redundant environment preparation. Improved message formatting and error handling.
  • Python-based functions (RunPAGA(), RunSCVELO(), RunPalantir(), RunCellRank(), RunWOT()) now automatically call PrepareEnv() internally, eliminating the need for users to manually prepare the Python environment before using these functions.
  • cluster_within_group2(): New function for clustering within groups.
  • Multiple plotting functions: Replaced geom_sankey() with ggsankey::geom_sankey() for better Sankey diagram support.
  • Multiple functions: Replaced ::: operator with get_namespace_fun() for safer namespace access.
• refactor:
  • Removed RunMonocle() function and related documentation (RunMonocle2.Rd, RunMonocle3.Rd).
  • Removed projection_functions.R file (functions moved to other locations).
  • Replaced custom theme functions with thisplot::theme_this() (exported as theme_scop()).
  • Replaced direct log_message() calls with thisutils::log_message() for consistency.
  • Removed palette_list data object.
• deps:
  • Moved cli from Suggests to Imports for better message formatting support.
  • Added thisplot to Imports for theme and utility functions.
  • Added ggsankey to Suggests for Sankey diagram support.
  • Added remote dependencies: theislab/destiny, mengxu98/thisplot.
  • Removed unused dependencies: Biobase, BiocGenerics, concaveman, DDRTree, glmGamPoi, hexbin, monocle, png, ragg, tidyr.
• docs:
  • Updated documentation across multiple functions to reflect code refactoring.
  • Improved code organization and maintainability.

scop 0.5.5

• bugs:
  • Fixed VelocityPlot() function error in plot_type = "grid" mode: replaced vectorized arrow length with fixed-length arrows (using mean length) to resolve vapply() error that occurred when grid::arrow() received a vector instead of a single value, see #72, #74.

scop 0.5.4

• bugs:
  • Fixed parameter name error in CheckDataType() function calls: changed data parameter to object in RunKNNMap(), RunSymphonyMap(), RunScmap(), RunPCAMap(), and RunSingleR() functions, see #68.
  • Fixed SingleCellExperiment object creation in RunScmap() and RunSingleR() functions: changed from coercing SummarizedExperiment to directly constructing SingleCellExperiment objects.

scop 0.5.3

• func:
  • PrepareDB(): Changed default Ensembl_version parameter from 103 to NULL for more flexible version handling.
  • Added Python version log_message() for Python-based functions (RunSCVELO(), RunPAGA(), RunPalantir(), RunCellRank(), RunWOT()) and added verbose parameter inheritance and improved message formatting using cli-style formatting.
• refactor:
  • Delete harmonizomeapi.py file.
  • Move scop_analysis.py into a single functions.py file in inst/python/ for better code organization and maintainability.
• docs:
  • Improved parameter documentation consistency.

scop 0.5.1

• docs:
  • Improved reference formatting and consistency across multiple functions.
  • Enhanced documentation clarity and readability.

scop 0.5.0

• func:
  • RunCellChat(): New function to perform CellChat analysis for investigating cell-to-cell communication with support for human, mouse, and zebrafish species.
  • CellChatPlot(): New function to visualize CellChat analysis results with various plot types and customization options.
  • Multiple integration functions: Improved error messages and message formatting for better user experience.
• deps:
  • Added CellChat package dependency with remote repository jinworks/CellChat.
• docs:
  • Updated README.md with improved code formatting and examples.
  • Enhanced documentation for cell communication analysis functions.
  • Improved error messages and user guidance across integration functions.
• refactor:
  • Removed some example figures to optimize package installation size.

scop 0.4.0

• func:
  • RunProportionTest(): New function to perform Monte-carlo permutation test for quantifying cell proportion differences between conditions.
  • ProportionTestPlot(): New function to generate proportion test plots with customizable significance thresholds and visualization options.
  • Multiple Python-based functions: add \dontrun{} blocks for Github workfolw checking.
• docs:
  • Added comprehensive documentation for new proportion testing functions.
  • Enhanced example documentation across multiple functions.
  • Updated package documentation and examples.

scop 0.3.4

• docs:
  • Updated workflow examples and function documentation.

scop 0.3.3

• func:
  • Multiple functions: Improved parameter documentation formatting and consistency across the package.

scop 0.3.2

• func:
  • GetFeaturesData() and AddFeaturesData(): Enhanced argument clarity, added input validation, and standardized return values for Seurat, Assay, and Assay5 objects.
  • CellCorHeatmap():
    • Renamed parameters: query_cell_annotation → query_annotation, ref_cell_annotation → ref_annotation.
    • Improved error message formatting using cli-style formatting.
    • Simplified variable assignments and improved readability.
• docs:
  • Comprehensive documentation updates across multiple functions including AnnotateFeatures, CellDimPlot, CellStatPlot, FeatureStatPlot, GroupHeatmap, RunCellQC, and others.
  • Improved parameter descriptions and function clarity.

scop 0.3.1

• func:
  • EnrichmentPlot() and GSEAPlot(): Removed conditional font face styling (face = ifelse() logic) for better text rendering consistency. Set the default value of lineheight from 0.5 to 0.7.
  • Updated check_r() function for improved package checking functionality.
  • Updated reexports functionality.
• docs:
  • Updated documentation formatting and consistency.

scop 0.3.0

• func:
  • Fixed segmentation faults and R crashes on M-series MacBook when running Python functions.
  • RunPAGA(): Enhanced with M-series MacBook detection and automatic environment configuration.
  • RunSCVELO(): Added ARM64-specific optimizations to prevent crashes and ensure stable execution.
  • RunCellRank(): Implemented M-series compatibility with proper NUMBA configuration.
  • RunPalantir(): Added ARM64 support with single-threaded execution mode.
  • RunWOT(): Enhanced with M-series MacBook environment variable settings.
  • RunTriMap(): Added M-series MacBook compatibility for dimensionality reduction.
  • RunPaCMAP(): Implemented ARM64-specific environment configuration.
  • RunPHATE(): Added M-series MacBook support for non-linear dimensionality reduction.
  • RunCellQC(): Enhanced both scrublet and doubletdetection functions with ARM64 compatibility.
• docs:
  • Updated function documentation to reflect M-series MacBook compatibility.
  • Added technical notes about ARM64 architecture considerations.

scop 0.2.9

• bugs:
  • Fix bug for RunSCVELO().
• docs:
  • Updated documentation for some functions.

scop 0.2.7

• func:
  • Added an internal function .check_pkg_status() to check if an R package is installed.
  • Update function CheckDataType() to S4 class function.
  • Update function standard_scop(), make it more efficient.
• data:
  • Delete lifemap data, including: lifemap_cell, lifemap_compartment and lifemap_organ.
  • Reconstructed the sample data for both panc8_sub and pancreas_sub, retaining only the basic Seurat object.

scop 0.2.6

• func:
  • Added remove_r() function for easy remove R packages.
  • Rename function: RemovePackages() to remove_python().
  • Removed other methods of installing R packages from the check_r() function, only retaining pak::pak.
  • Delete useless import packages: BBmisc, BiocManager, covr, devtools, promises and withr.
  • Optimize the structure of _pkgdown.yml file.
• docs:
  • Updated documentation for some functions.

scop 0.2.5

• func:
  • Rename function: palette_scop() to palette_colors().

scop 0.2.4

• func:
  • Rename functions: check_srt_merge() to CheckDataMerge(), check_srt_list() to CheckDataList and check_data_type() to CheckDataType.

scop 0.2.2

• func:
  • Replace all BiocParallel::bplapply() with thisutils::parallelize_fun().
• bugs:
  • Fix bugs in RunSingleR().

scop 0.2.0

• func:
  • Added remove_python() function for easy remove Python packages.
• bugs:
  • Corrected an issue in py_to_r2() function (intrinsic function), which ensures that Python-dependent functions like RunPAGA() and RunSCVELO() function run correctly.

scop 0.1.9

• func:
  • Update CellScoring() and AddModuleScore2() functions. Now, new parameters cores and verbose have been added.
  • AddModuleScore2() function no longer uses the BiocParallel::bpparam() function to enable parallelization, but thisutils::parallelize_fun, and the cores parameter is used to control the number of cores in thisutils::parallelize_fun.

scop 0.1.5

• bugs:
  • Fix error for RunPalantir() function, see #23.

scop 0.1.4

• func:
  • Update .onAttach(), now .onAttach() will print more information about conda and Python.
  • Update PrepareEnv() function for easy add or update a conda environments and install Python packages.
  • Added ListEnv() and RemoveEnv() functions for easy management of conda environment and Python packages.

scop 0.1.3

• func:
  • Added TACSPlot() function for creating FACS-like plots. Please refer to Kernfeld et al. paper and Github for specific information.

scop 0.0.9

• bugs:
  • Fix a bug for PrepareEnv() function.
  • The default Python version is now set to 3.10-1.

scop 0.0.6

• func:
  • Add GetAssayData5() function, a reimplementation of GetAssayData(), for compatibility with Seurat v5 Assay objects.
  • Updated GetFeaturesData() and AddFeaturesData() function to support retrieving and adding feature metadata.

scop 0.0.5

• data:
  • Updated the pancreas_sub and panc8_sub test datasets to the Seurat v5 object format.