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SpaMTP (developmental)

  • Spatial pathway plots now retain labelled placeholder panels for pathways with no measured features or finite z-scores, preventing empty-data errors in the Mouse Brain vignette. Unknown pathway names report a clear error.

  • Restored standalone resource loading for the public GitHub release. RaMP databases and corrected topology collections are bundled, along with precomputed SMILES features. Installation, default annotation and pkgdown builds no longer require SpaMTPdb, SpaMTPData, or Hub registration. LoadSpaMTPDatabase() keeps support for custom bundles and local RDS files; SpaMTPDatabaseInfo() now describes the bundled snapshot. The separate Bioconductor submission retains its companion-package architecture.

  • Fixed pathway interaction corruption in the graphite-derived RaMP 3.0.7 graphs. A pinned, checksum-guarded correction restores per-edge source labels, directions, and parallel interactions for KEGG, Reactome, WikiPathways and SMPDB. Interaction styles now use label semantics across databases, and undirected edges have no arrowhead. The original published resource bytes retain their checksums; SpaMTP applies corrections when loading them.

  • Added the Pathway Database Integration vignette, a reproducible correction builder, source checksums, and regression tests for the Cell Cycle report.

  • Parallel pathway interactions now use separate curves, including reciprocal edges and self-loops, so each restored interaction can be inspected by hover. Routes remain stable when switching between focused and full networks.

  • Vignette builds no longer depend on AnnotationHub having ingested SpaMTPdb. The documentation workflow stages the RaMP 3.0.7 resources once from their immutable Zenodo deposition (doi:10.5281/zenodo.22045311), verifies each file against the manifest size and MD5, and exposes the directory to every article through SPAMTPDB_RESOURCE_DIR.

  • Documentation fixes for R CMD check: DOI references use \doi{} rather than raw \href{} links, ppm_range_match() has a single-line title, and the R sources and .Rd files are ASCII-only.

  • Declared the Transcriptomics and Alignment biocViews.

  • Split versioned resources from the analysis code: SpaMTPdb now supplies the pruned RaMP annotation and pathway snapshot, and SpaMTPData provides named access to large experiment/vignette objects. LoadSpaMTPDatabase() and SpaMTPDatabaseInfo() form the public database interface. The software package retains only the small adduct and reaction-style constant tables.

  • Updated the package citation to the peer-reviewed Nature Methods paper, designated Tianyao Lu as the current package maintainer, and added direct links to the developmental documentation and source branch. Andrew Causer remains credited as an original author and former maintainer.

  • Added ApplySpatialAlignment() to apply existing SMINT coordinate outputs or homogeneous transforms, estimate landmark-based affine alignment in R, and run the SMINT-compatible STalign LDDMM workflow through an optional Python backend. Alignment provenance and nearest-target diagnostics are retained in the returned SpaMTP object without storing large Python velocity tensors.

  • Pathway enrichment, pathway-assay construction, Fisher analysis of m/z inputs, and interactive pathway networks now consume the scored Ramp_IDs produced by the indexed annotation engine. AnnotateSM() resolves the versioned RaMP 3.0.7 chemical-property table through SpaMTPdb, records annotation provenance in @tools$mz_annotation, and retains @tools$db_3 only for compatibility. Legacy annotations require an explicit annotation_source fallback.

  • Annotation candidates can now be stored once with AnnotateSM(min_score = 0) and filtered later with annotation_score_threshold. Interactive pathway networks add metabolite_detection = "annotated" to display score-filtered pathway metabolites without requiring DE significance, while retaining separate leading-edge evidence in node styling and tooltips.

  • Moved the pruned RaMP snapshot from 2.5.4 to versioned SpaMTPdb 3.0.7 resources, with explicit upstream/source metadata and reproducible resource staging scripts.

  • Added a chemically validated adduct rule table and reusable sorted m/z index.

  • Added ppm pruning, proton/charge bounds, mass-defect scoring, isotope checks, and contextual adduct-family scoring while retaining the legacy annotation result columns.

  • Added dependency-free SMILES graph decomposition, functional-group and atom site reporting, mode-specific protonation/deprotonation and alkali-binding priors, and PredictAdductsFromSMILES(). Aromatic functional groups are perceived consistently from both lowercase aromatic and alternating-bond six-membered Kekule SMILES. Full RaMP runs join an independent precomputed SpaMTPdb::smiles_features resource; small custom databases are inferred automatically at runtime.

  • chem_props can now be used directly as a RaMP-backed annotation database.

  • Rebuilt PathwayNetworkPlots() around cached topology lookup, precomputed edges, selective sparse-matrix extraction, and JSON serialization. The new responsive viewer adds zoom/pan, focused/full networks, label controls, shared reaction markers, spatial inspection, and SVG export.

  • Made legacy pathway annotation robust to unequal Isomers_IDs and IsomerNames counts, and added a cached Mouse Brain/DHB network demo.

  • Pathway network metabolite labels now remain visible in the default label mode; dragged nodes stay pinned until released, and edge legends persist when the focused view changes.

  • Added interactive repulsion, balanced-force, radial, and gene/metabolite pathway layouts, with a more widely spaced repulsion layout as the default.

  • Harmonised all versioned pathway-graph node IDs with RaMP-DB 3.0.7, added a reproducible cross-version graph updater/auditor, and added stable source-ID labels when RaMP itself has no common name.

SpaMTP 1.1.0

Updated SpaMTP Release (Oct 2025)

Additional Features:

  • Updated LoadSM() function for compatability with Cardinal V3.8
  • Implementation of GraphPCA in R.
  • Additional functions for handling large datasets - AnnotateBigData and SelectROI.
  • Function for refining m/z annotations based on correlated pathway activity or MS/MS profiles.
  • Package wide update for compatability with Cardinal V3.8 and Seurat V5.3.

SpaMTP 1.0.0

  • Initial SpaMTP Release (March 2025)