NEWS

SpaceMarkers 2.0.0

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.