NEWS

SpaceMarkers 2.3.1

Added SpaceMarkersExperiment (SME), an S4 class extending SpatialExperiment that carries hotspots, influence maps, and pattern metadata alongside expression and spatial coordinates.
Added SME-aware methods and dispatch for get_spatial_features, get_interacting_genes, get_pairwise_interacting_genes, and related accessors so users can stay in a single Bioconductor object end-to-end.
Re-exported SpatialExperiment / SummarizedExperiment accessors so SME workflows do not require attaching upstream packages.

Added load_anndata() to read .h5ad files directly into a SpaceMarkersExperiment.
Added save_anndata() to write SME objects back to .h5ad with round-trip fidelity.
Added direct SingleCellExperiment → SpaceMarkersExperiment coercion.

Added overlap_map() for per-spot directed interaction classification (3-level factor per direction).
plot_spatial() gained a source argument (colData/assay/hotspots/influence_map/interaction) and directed interaction labels for three-way hotspot overlays.
Hotspot plots in vignettes now use distinct colors per pattern.

New SpaceMarkersExperiment_vignette walks through the SME-first workflow.
SpaceMarkersStepByStep_vignette restructured as a tutorial with per-step plots interleaved with narrative.
Vignette data downloads now route through BiocFileCache instead of ad hoc temp files.
Compact JPEG raster output keeps rendered HTML vignettes under Bioconductor's per-file size guideline.

Runnable examples and \value sections added across exported functions for BiocCheck.
Tightened .Rbuildignore and .gitignore for a clean source tarball.
Renamed R/OneSpaceMarkers.R → R/SpaceMarkers.R and regenerated Collate order.

Avoided dense coercion in the gene filter and skipped materializing the spPatterns data frame, reducing memory pressure on large samples.

Added support for directed cell-cell interaction (see calculate_gene_scores_directed, calculate_influence)
Functions for supporting ligand-receptor interactions based on directed cell-cell interactions
Added ligand–receptor and gene-set scoring utilities: calculate_lr_scores, calculate_gene_set_score, and calculate_gene_set_specificity.
Added support for handling Visium HD
plotting functions using circlize for showing ligand-receiver interactions.
API and naming standardization (backwards-incompatible) Major public functions renamed to snake_case for consistency (examples: calcInfluence → calculate_influence, getInteractingGenes → get_interacting_genes, getPairwiseInteractingGenes → get_pairwise_interacting_genes, getSpatialFeatures → get_spatial_features, getSpatialParameters → get_spatial_parameters)

Added findAllHotspots to use with getPairwiseInteractingGenes
Return empty interacting genes list instead of failing with error when no genes pass fdr threshold.

Updated SpaceMarkersMetric by fixing signage and log transformed to scale magnitude
Added get_spatial_paramsExternal which enables getting spatial parameters from file or from the user.
Deprecated getSpatialParameters
Enabled includeSelf = TRUE in getInteractingGenes.R to improve hotspot detection
Enabled load10XCoords to read coordinates from VisiumHD directory
Optimized the long running row.dunn.test() function
Corrected sparse -> dense conversions
Added getPairwiseInteractingGenes which enables pairwise analysis of interacting patterns
getSpatialFeatures: add default method to infer the object passed to it.