ARBO 1.0.1

Added Zenodo DOI information for software citation.
Added image origin and usage notes for the artificially constructed MSI dataset.

ARBO 1.0.0

First stable 1.0.0 release of ARBO.

ARBO 0.5.1

Updated SEMs_screen() to better handle different output structures returned
by Cardinal::colocalized().

ARBO 0.5.0

• Added two UMAP input strategies in spatial_clustering_workflow():
  • "scaled" for min-max scaled spectra
  • "l2_pca" for row-wise L2-normalized spectra followed by PCA with irlba
• Added pca_n_components to control the number of retained principal components
  in the "l2_pca" workflow.
• Enforced metric = "euclidean" when umap_input_method = "l2_pca".

ARBO 0.4.1

Added parallel execution support for Python UMAP via n_jobs.

ARBO 0.4.0

• Rename the package to ARBO.
• Update package metadata and documentation.
• Refine clustering workflows and result integration into Cardinal MSI objects.

spatMetaCluster 0.3.1

Modify vignettes

spatMetaCluster 0.3.0

• add SEMs_screen() for spatially enriched metabolites screening
• add image2ggplot() to reconstruct Cardinal::image() output with ggplot2
• add msi_img_overlay() for layered MSI image overlay with internal legend handling
• update cherry_tomato_msi with additional m/z annotations and regenerated object
• add metabolites that are not region-enriched distributions

spatMetaCluster 0.2.0

run_kmeans_cluster → run_clustering
spatial_kmeans_workflow → spatial_clustering_workflow
minmax_normalize → apply_feature_scaling
run_umap_py with more flexible n_components

spatMetaCluster 0.1.1

v0.1.1

Update package functions and documentation