NEWS

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smotif 0.2.0

• motif_enrichment_stream(): enrichment over an Arrow stream of edges, with labels passed as a lookup keyed by integer node id. The network's nodes are the stream's endpoints. Needs smotifrs >= 0.2.0.

smotif 0.1.0

Initial scaffold of the smotif package for spatial multi-cellular motif discovery in spatial omics data.

In scope for v0.1

• SpatialGraph S3 class with parquet round-trip via arrow.
• build_spatial_graph() over coordinates with kNN, Delaunay, and radius methods.
• Motif enumeration (size 2 and 3 closed/open, size 4 via igraph::motifs) with colored canonical labeling for cell-typed nodes.
• Spatially-aware null models: label permutation, region-stratified label permutation, geometric jitter.
• Empirical enrichment testing with BH adjustment.
• Wilcoxon and module-score gene association at motif and orbit level.
• Cross-region and cross-sample motif comparison.
• Reference dataset preparation script (inst/scripts/prepare_workshop_xenium.R) for the workshop Xenium human lung cancer FFPE slide.

Out of scope for v0.1 (planned later)

• Rust / extendr backend (a # TODO(rust-backend) marker in R/motifs.R flags the dispatch site).
• Motifs of size 5 or larger.
• Directed motifs, hypergraphs, motif embeddings.
• Per-sample meta-analysis in associate_genes().
• Visualization beyond plot.Motifs().
• Giotto Suite integration (intended as a separate downstream package).
• Full geometric resampling null with re-thresholding.