Changes in version 1.9.2                        

Bug fixes

  - Corrected the robust local z-score calculation in localOutliers().
    Scores now use the focal spot value and the unscaled median absolute
    deviation of neighboring spots, matching the published method.
    Previous versions applied the normal-consistency scaling twice and
    could associate a neighbor's score with the focal spot.
  - Removed the spatialEco dependency, which is no longer needed for
    local z-score calculation.

Seurat compatibility

  - Reworked Seurat support around small, tested object adapters that
    preserve spot names and ordering and use public SeuratObject
    accessors.
  - Added integration tests for localOutliers(), spatial-coordinate
    extraction, metadata replacement, subsetting, and
    flagVisiumOutliers() with real Seurat objects.
  - Added explicit guidance when findArtifacts() is used with data
    lacking mitochondrial signal, including Visium FFPE probe-panel
    data.

                        Changes in version 1.5.0                        

Major Features

  - Seurat Compatibility: Added comprehensive compatibility layer
    enabling SpotSweeper functions to work seamlessly with Seurat
    spatial objects alongside existing SpatialExperiment support. This
    major enhancement expands SpotSweeper's usability across the spatial
    transcriptomics ecosystem.
  - Flexible Coordinate Systems: Enhanced localOutliers() to support
    custom coordinate systems for neighborhood detection, enabling
    outlier detection in PCA, UMAP, or any reduced-dimension space.

New Functions

  - getSpatialCoords(): Universal function to extract spatial
    coordinates from both SpatialExperiment and Seurat objects
  - getMetadata(): Universal function to access metadata
    (colData/meta.data) from both object types
  - setMetadata(): Universal function to update metadata in both object
    types
  - subsetSpatialObject(): Universal subsetting function for both object
    types
  - validateMetadataColumns(): Validation function to ensure required
    columns exist
  - is_seurat() and is_spatial_experiment(): Object type detection
    functions

Enhanced Functions

  - localOutliers():
      - Now accepts both SpatialExperiment and Seurat objects with
        automatic detection
      - New coords parameter allows custom coordinate matrices for
        neighborhood detection
      - Default behavior unchanged (uses spatial coordinates)
      - Supports PCA, UMAP, t-SNE, or any coordinate system for neighbor
        finding

Bug Fixes

  - Fixed focal spot inclusion: Removed focal spot from neighborhood
    when calculating modified z-scores in localOutliers() to prevent
    circular logic and bias, resulting in more accurate outlier
    detection.

Documentation

  - Updated function documentation to reflect dual compatibility and new
    coordinate options
  - Added Seurat usage examples alongside existing SpatialExperiment
    examples
  - Added examples for custom coordinate systems (PCA, UMAP)
  - Comprehensive test suite for compatibility layer and coordinate
    functionality

                        Changes in version 1.3.2                        

New Features

  - Added the 'flagVisiumOutliers()' function to identify and flag
    systematic outlier spots in Visium datasets. This feature enhances
    data quality by allowing users to efficiently detect and exclude
    problematic spots from downstream analyses.

Minor Changes

  - Broadened Compatibility: Updated all functions to use inherits(spe,
    "SpatialExperiment") instead of checking class(spe) directly. This
    change ensures that derived classes (e.g., SpatialFeatureExperiment)
    are also supported, improving flexibility and ease of use.

                        Changes in version 1.3.1                        

Major Changes

  - Function Renaming: The function plotQC has been renamed to
    plotQCmetrics to better reflect its purpose. The new function
    plotQCmetrics should be used moving forward. This change improves
    clarity in the package’s API by specifying that this function is
    designed for plotting QC metrics.

New Features and Enhancements

  - shape argument: Added a shape argument to findArtifacts, allowing
    users to specify the neighborhood shape as either "hexagonal" or
    "square" for local variance calculations. This enhancement provides
    flexibility for different spatial arrangements in spatial
    transcriptomics data.

  - Updated n_order parameter: Renamed the n_rings parameter to n_order
    in the findArtifacts function to better describe its purpose of
    specifying the N-order neighbors for local mitochondrial variance
    calculations.

  - Parallelization: Added a workers argument for parallel processing
    using BiocParallel in both localOutlier and localVariance functions.
    This allows for faster computation, particularly on larger datasets.

Deprecations

  - plotQC Function Deprecated: The plotQC function is now deprecated.
    While it remains available for backward compatibility, users are
    encouraged to transition to plotQCmetrics. Calling plotQC will
    display a warning, reminding users of the deprecation.

This change is backward compatible; existing code using plotQC will
still work but will show a warning. We recommend updating your code to
use plotQCmetrics to avoid any issues in future versions where plotQC
may be removed.