Changelog

Source: NEWS.md

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.