Package: SpaMTP 0.99.10

Tianyao Lu

SpaMTP: Spatial Metabolomics and Multi-Omics Analysis

Provides analysis, annotation, visualisation, and multi-omic integration methods for spatial metabolomics data. SpaMTP interoperates with Cardinal and SpatialExperiment containers, with optional Seurat conversion; supports indexed accurate-mass annotation using versioned RaMP resources; and implements spatial feature analysis, pathway enrichment, pathway-network visualisation, and alignment with spatial transcriptomics data.

Authors:Andrew Causer [aut], Tianyao Lu [aut, cre], Christopher C.J. Fitzgerald [aut], GML Lab [lbr], Brain Cancer Research Lab [lbr], UQ Institute [fnd], QIMR Institute [fnd], WEHI Institute [fnd]

SpaMTP_0.99.10.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpaMTP/json (API)

# Install 'SpaMTP' in R:

install.packages('SpaMTP', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/spamtp-project/spamtp/issues

Pkgdown/docs site:https://genomicsmachinelearning.github.io

Datasets:

adduct_file - Common adduct constants
reaction_type - Pathway-network reaction styles

On CRAN:

massspectrometry imagingmassspectrometry metabolomics spatial transcriptomics alignment

4.45 score 20 scripts 107 exports 220 dependencies

Last updated from:2c54b7bdef. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	299
linux-devel	OK	626
source / vignettes	OK	2358
linux-release	OK	615
macos-release	OK	508
macos-oldrel	OK	421
windows-devel	OK	595
windows-release	OK	569
windows-oldrel	OK	584
wasm-release	OK	255

Exports:addCustomMZAnnotations addFMP10Annotations addSMImage addSpatialImage addSSCAnnotation addTranscriptome adductRules alignSpatialOmics analyzeSpaMTPRegions annotateBigData annotateGeneIdentifiers annotateMZ annotateSM annotateSMILESStructure annotationInfo applySpatialAlignment asCardinal asSpatialExperiment binMetabolites binnedCardinalToSeurat binSpaMTP buildGeneMappingIndex buildMZAnnotationIndex buildPathwayIndex calculateAnnotationStatistics calculateSingleAnnotationStatistics cardinalToSeurat cardinalToSpatialExperiment checkAlignment combineTransformations convertSeuratToCardinal createMergedModalityAssay createPathwayAssay createPathwayObject deconvolveSMILES demsHeatmap densityMap findAllDEMs findCorrelatedFeatures findDuplicateAnnotations findNearestMZ findRegionalPathways findSpatiallyVariableMetabolites fishersPathwayAnalysis getKmeanClusters getMetaspace getMZMetadata getRefinedAnnotations getSpatiallyVariableMetabolites getSquareCoordinates imageMZAnnotationPlot imageMZPlot interactiveSpatialPlot kNeighborsGraph loadMetaspace loadSM loadSpaMTPDatabase maldiMatrixProfiles maldiMatrixRules mapGeneIdentifiers mapSpatialOmics massIntensityPlot metaspaceClient metaspaceToFeatureMatrix multiOmicIntegration mzBoxPlot mzRidgePlot mzViolinPlot normalizeSMData pathwayNetworkPlots pixelPlot plot3DFeature plotPathways plotPathwaysSpatially plotRegionalPathways plotSinglePathway plotSinglePathwaySpatially plotSpatialFeature predictAdductsFromSMILES queryMZAnnotationIndex readSMMatrix refineLipids renderSpaMTPReport runDE runMetabolicPCA runPooling runRAMPGeseca runSpaMTPWorkflow runSpatialGraphPCA savePheatmapAsPDF saveSpaMTPData scaleSMData searchAnnotations selectROIs seuratToSingleCellExperiment seuratToSpatialExperiment spaMTPDatabaseInfo spatialExperimentToCardinal spatialExperimentToSeurat spatialMZAnnotationPlot spatialMZPlot spectralBinning statPlot subsetMZFeatures subsetSPM tmmNormalize visualisePathways

Dependencies:abind affy affyio AnnotationDbi AnnotationFilter AnnotationHub ape askpass assorthead base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocManager BiocNeighbors BiocParallel BiocSingular BiocVersion Biostrings bit bit64 blob bluster bslib cachem Cardinal CardinalIO class classInt cli clue cluster codetools commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doParallel dplyr dqrng DropletUtils e1071 edgeR evaluate farver fastmap fastmatch fgsea filelock FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggbeeswarm ggdendro ggplot2 ggrepel ggridges globals glue gridExtra gtable h5mread HDF5Array highr htmltools htmlwidgets httpuv httr httr2 igraph impute IRanges irlba isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma listenv locfit magick magrittr MALDIquant MASS Matrix MatrixGenerics matrixStats matter mclust memoise MetaboCoreUtils metapod mime MsCoreUtils MSnbase MultiAssayExperiment mzID mzR naturalsort ncdf4 nlme ontologyIndex openssl otel parallelly pcaMethods pheatmap pillar pkgconfig plotly plyr png preprocessCore promises ProtGenerics proxy PSMatch PTMods purrr QFeatures R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress reshape2 rgoslin rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSpectra RSQLite rsvd Rtsne s2 S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scran scuttle Seqinfo sf shiny SingleCellExperiment sitmo snow sourcetools SpaMTPdb SparseArray sparseMatrixStats SpatialExperiment Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex units utf8 uwot vctrs vipor viridis viridisLite vsn withr wk xfun XML xtable XVector yaml

SpaMTP: Modern Data Access and Workflow Migration

Rendered fromModern_Data_Access.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-13

Auditable gene mapping with SpaMTPdb and SpaMTPData

Reference ownership and reproducibility | Build once, inspect before testing | Annotate experiment features without altering expression | Use the whole measured panel as the universe | One membership index for enrichment, expression and plots

Rendered fromGene_Identifier_Mapping.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-13

Designing and evaluating a spatial multi-omics workflow

Analysis questions determine the workflow | Supply modalities and study design explicitly | Compare representations using the same observations and features | Region characterization is richer than a mean difference | Keep biological-replicate inference separate | Ask whether colocalization survives regional composition | Map identities before pathway statistics | Run the real mouse-brain reference recipes | Render and retain a reviewable analysis

Rendered fromEnd_to_End_Workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-21

Pathway databases, interaction provenance, and rebuilding graphs

Membership and topology are separate resources | Identifier consolidation | Interaction correction | Loading and inspecting corrected graphs | Reproducing the correction

Rendered fromPathway_Database_Integration.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-21

SpaMTP, SpaMTPdb and SpaMTPData: A Native Companion Workflow

Clear responsibilities | Data to a native analysis container | Database discovery without network access | Annotate without inventing a downloaded database | Published native datasets and historical archives

Rendered fromSpaMTP_Companion_Workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-13

SpaMTP: Indexed Metabolite Annotation with RaMP 3.0

Rendered fromMetabolite_Annotation_Pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-09-13

SpaMTP: Spatial Metabolite Annotation

Rendered fromSpaMTP_Bioconductor.Rmdusingknitr::rmarkdown

Last update: 2026-09-22
Started: 2026-08-14

Help page	Topics
Adds in backslashes required to take into account special using grepl such as brackets and +	add_backslashes_to_specialfeatures
Assign custom annotations to m/z values	addCustomMZAnnotations
Annotates FMP10 matrix data	addFMP10Annotations
Attach and optionally align an optical image to MSI	addSMImage
Add an image using SpatialExperiment infrastructure	addSpatialImage addSpatialImage,SpatialExperiment-method
Adds Cardinal ssc segmentation annotation to m/z count data object	addSSCAnnotation
Store a paired transcriptome as an alternative experiment	addTranscriptome addTranscriptome,SpatialExperiment-method
Common adduct constants	adduct_file
Return the validated SpaMTP adduct rule table	adductRules
Align two spatial experiments using an affine transformation	alignSpatialOmics
Add region summaries and native spatial analyses to a workflow result	analyzeSpaMTPRegions
Annotates vector of m/z values	annotateBigData
Store gene mapping in a native experiment's row metadata	annotateGeneIdentifiers
Annotate one or more observed m/z values	annotateMZ
Annotates m/z values stored in a SpaMTP Object	annotateSM
Add SMILES-derived structural features to a metabolite database	annotateSMILESStructure
Annotates m/z values stored in a data.frame based on reference metabolite dataset	annotateTable
Inspect the metabolite annotation provenance stored in a SpaMTP object	annotationInfo
Apply automatic or precomputed spatial alignment	applySpatialAlignment
Convert a SpatialExperiment to a Cardinal experiment	asCardinal asCardinal,MSImagingArrays-method asCardinal,MSImagingExperiment-method asCardinal,SpatialExperiment-method
Convert an object to a SpatialExperiment	asSpatialExperiment asSpatialExperiment,MSImagingArrays-method asSpatialExperiment,MSImagingExperiment-method asSpatialExperiment,SpatialExperiment-method asSpatialExperiment,SummarizedExperiment-method
Sum selected metabolite features per pixel	binMetabolites
Convert a binned Cardinal matrix to an optional Seurat object	binnedCardinalToSeurat
Bin aligned spatial metabolomics features	binSpaMTP binSpaMTP,ANY-method binSpaMTP,MSImagingArrays-method binSpaMTP,MSImagingExperiment-method binSpaMTP,SpatialExperiment-method
Build a gene identity index from RaMP and HGNC	buildGeneMappingIndex
Build a reusable indexed metabolite annotation search space	buildMZAnnotationIndex
Build a shared, auditable pathway membership index	buildPathwayIndex
Calculates the mz range of the observed_df	calculate_bounds
Rank annotations for all MSI features	calculateAnnotationStatistics
Rank candidate metabolite annotations using paired pathway expression	calculateSingleAnnotationStatistics
Convert a Cardinal object to an optional Seurat object	cardinalToSeurat
Convert an aligned Cardinal experiment to SpatialExperiment	cardinalToSpatialExperiment
Checks if the complete adduct is in the data base, else returns a truncated adduct	check_and_truncate_adduct_vector
Check Cardinal Version	check_cardinal_version
Inspect the alignment of two spatial experiments	checkAlignment
Combines rigid tranformation matrices	combineTransformations
Convert an optional Seurat object to Cardinal	convertSeuratToCardinal
Combine paired modalities in a scaled alternative experiment	createMergedModalityAssay
Create a RaMP identity alternative experiment	createPathwayAssay
Store pathway scores in an alternative experiment	createPathwayObject
Filters the provided metabolomic database by polarity and adducts	db_adduct_filter
Decompose explicit functional groups in SMILES strings	deconvolveSMILES
Heatmap of Differentially Expressed Metabolites	demsHeatmap
Export an interactive spatial detection-density viewer	densityMap
Access SpaMTP data through Bioconductor containers	experimentAccess
Finds differentially expressed m/z values/metabolites between all comparison groups.	findAllDEMs
Find features correlated with a metabolite, gene, or pixel group	findCorrelatedFeatures
Finds if any metabolite is duplicated across multiple m/z values.	findDuplicateAnnotations
Finds the nearest m/z peak to a given value in a SpaMTP Object	findNearestMZ
Regional Pathway Enrichment	findRegionalPathways
Find spatially variable metabolites using Moran's I	findSpatiallyVariableMetabolites
Fisher Exact Tests for Pathway Enrichment	fishersPathwayAnalysis
Filters reference Database to only select natural elements	formula_filter
Helper function for building a pathway db based on detected	get_analytes_db
Perform K-means clustering on a specified reduction	getKmeanClusters
Core METASPACE Data Retrieval	getMetaspace
Gets values from a single metadata column for a respective m/z value.	getMZMetadata
Refines and reduces m/z annotations	getRefinedAnnotations
Get the top spatially variable metabolites	getSpatiallyVariableMetabolites
This function computes the coordinates of a square's four corners based on a given center point and width.	getSquareCoordinates
Plot annotated metabolites without an optical image	imageMZAnnotationPlot
Plot MSI features from a Bioconductor spatial container	imageMZPlot
Interactively inspect mass windows in a spatial experiment	interactiveSpatialPlot
Construct a k-Nearest Neighbour Graph from Spatial Coordinates.	kNeighborsGraph
Filters the annotation list to only include the first n number of annotations per m/z	labels_to_show
Load METASPACE Data as a SpatialExperiment	loadMetaspace
Load imzML data into a Bioconductor-native spatial container	loadSM
Load versioned SpaMTP annotation resources	loadSpaMTPDatabase
List MALDI matrix and on-tissue derivatization profiles	maldiMatrixProfiles
Select annotation rules from the MALDI matrix/reagent profile	maldiMatrixRules
Map gene identifiers with an auditable HGNC identity	mapGeneIdentifiers
Map metabolite intensities to transcriptomic pixels or cells	mapSpatialOmics
Plot mean mass spectra from a native spatial experiment	massIntensityPlot
Metaspace R Client Constructor	metaspaceClient
Convert METASPACE Images to Feature Matrix	metaspaceToFeatureMatrix
Integrate paired modalities using native PCA embeddings	multiOmicIntegration multiOmicIntegration,ANY-method multiOmicIntegration,SpatialExperiment-method
Generates a Boxplot of spatial metabolic intensity data	mzBoxPlot
Generates a ridge plot of spatial metabolic intensity data	mzRidgePlot
Generates a violin plot of spatial metabolic intensity data	mzViolinPlot
Normalize spatial metabolomics intensity data	normalizeSMData normalizeSMData,ANY-method normalizeSMData,MSImagingArrays-method normalizeSMData,MSImagingExperiment-method normalizeSMData,SingleCellExperiment-method
Construct an interactive pathway network visualization	pathwayNetworkPlots
Convert point symbols to squares without changing coordinates or scales	pixelPlot
Compare two spatial features in 3D	plot3DFeature
Plot named pathways on a dimensionality reduction	plotPathways
Plot named pathways in tissue coordinates	plotPathwaysSpatially
Plot significantly enriched pathways per region	plotRegionalPathways
Plot a pathway score on a Bioconductor dimensionality reduction	plotSinglePathway
Plot a pathway score in tissue coordinates	plotSinglePathwaySpatially
Plot spatial features from a Bioconductor container	plotSpatialFeature plotSpatialFeature,MSImagingExperiment-method plotSpatialFeature,SpatialExperiment-method
Calculates the ppm error as a valve	ppm_error
Check whether m/z values match within a ppm tolerance	ppm_range_match
Predict a structure-aware adduct search space from SMILES	predictAdductsFromSMILES
Print an indexed metabolite annotation search space	print.spamtp_mz_index
Find all library spectra10 above a cosine threshold for each imaging peak, restricting to a global precursor-mz range.	Pseudo_msms
Query an indexed metabolite annotation search space	queryMZAnnotationIndex
Pathway-network reaction styles	reaction_type
Read a binned spatial metabolomics matrix	readSMMatrix
Uses common lipid nomenclature to simplify lipid annotations	refineLipids
Render a portable, self-contained multi-omics report	renderSpaMTPReport
Run limma contrasts on log-transformed technical pools	runDE
Compute PCA with scater on a selected experiment	runMetabolicPCA
Pools Bioconductor experiment into random pools for pseudo-bulking.	runPooling
Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis using the RAMP_DB metabolite/gene database.	runRAMPGeseca
Run a reproducible spatial multi-omics workflow and HTML report	runSpaMTPWorkflow
Perform Dimensionality Reduction using Graph-Regularised PCA on Spatial Data	runSpatialGraphPCA
Saves a demsHeatmap as a PDF	savePheatmapAsPDF
Export an experiment's expression matrix and metadata	saveSpaMTPData
Centre and scale features within a Bioconductor experiment	scaleSMData
Find Annotation	searchAnnotations
Launch an Interactive ROI Annotation App for SpatialExperiment	selectROIs
Convert Seurat expression data to SingleCellExperiment	seuratToSingleCellExperiment
Convert a Seurat object to SpatialExperiment	seuratToSpatialExperiment
Inspect SpaMTP database resources	spaMTPDatabaseInfo
Convert a SpatialExperiment to Cardinal	spatialExperimentToCardinal
Convert a SpatialExperiment to an optional Seurat object	spatialExperimentToSeurat
Plot annotated metabolites with optional optical images	spatialMZAnnotationPlot
Plot MSI features with optional optical images	spatialMZPlot
Spectral binning of intensity values stored in a Matrix object, converted from matter.	spectralBinning
Helper function for QC plots by generating intensity count data	statPlot
Subset a Bioconductor experiment by a list of m/z's	subsetMZFeatures
Subset features and pixels through Bioconductor containers	subsetSPM
Performs TMM normalization between categories based on a specified ident	tmmNormalize
Visualise Significant Pathways	visualisePathways

Package: SpaMTP 0.99.10

SpaMTP: Spatial Metabolomics and Multi-Omics Analysis

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