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url: https://genomicsmachinelearning.github.io/SpaMTP/
home:
title: SpaMTP
authors:
Andrew Causer:
href: https://github.com/agc888
Tianyao Lu:
href: https://github.com/BCRL-tylu
Christopher C.J. Fitzgerald:
href: https://github.com/ChemCharles
GML Lab:
href: https://github.com/GenomicsMachineLearning
html: <img src='man/figures/GML_invert.png' height='50' alt=''/>
Brain Cancer Research Lab:
href: https://www.wehi.edu.au/laboratory/brain-cancer-research-lab/
html: <img src='https://thebraincancercentre.org.au/wp-content/uploads/2022/09/BCC-WEHI-logo-horiz-RGB3.svg'
height='30' alt='WEHI Logo'/>
WEHI Institute:
href: https://www.wehi.edu.au/laboratory/brain-cancer-research-lab/
html: <img src='https://upload.wikimedia.org/wikipedia/en/7/7d/Wehi-logo-2020.png'
height='30' alt='WEHI Logo'/>
UQ Institute:
href: https://imb.uq.edu.au/research-groups/nguyen
html: <img src='https://upload.wikimedia.org/wikipedia/en/8/8c/Logo_of_the_University_of_Queensland.svg'
height='30' alt='University of Queensland Logo'/>
QIMR Institute:
href: https://www.qimrberghofer.edu.au/our-research/infection-and-inflammation/genomics-and-machine-learning-lab-2/
html: <img src='https://upload.wikimedia.org/wikipedia/commons/5/5a/Logo_of_the_QIMR.png'
height='30' alt='QIMR Logo'/>
footer:
roles:
- aut
- cre
sidebar:
roles:
- aut
- cre
- lbr
- fnd
template:
bootstrap: 5
light-switch: yes
bootswatch: flatly
bslib:
pkgdown-navbar-bg: '#212F3F'
body-secondary-color: '#18BC9C'
navbar:
structure:
left:
- intro
- reference
- articles
- news
right:
- search
- paper
- development
- github
- lightswitch
components:
paper:
text: Paper
href: https://doi.org/10.1038/s41592-026-03140-8
aria-label: SpaMTP Nature Methods paper
development:
text: Developmental
menu:
- text: Developmental documentation
href: https://genomicsmachinelearning.github.io/SpaMTP/developmental/
- text: Developmental source branch
href: https://github.com/GenomicsMachineLearning/SpaMTP/tree/developmental
news:
text: "Updates"
href: news/index.html
github:
icon: fa-github
href: https://github.com/GenomicsMachineLearning/SpaMTP
aria-label: GitHub
articles:
text: Vignettes
menu:
- text: Spatial Metabolomics Analysis
href: articles/Mouse_Urinary_Bladder.html
- text: Spatial Multi-Omics Analysis
href: articles/Multi-Omic_Mouse_Brain.html
- text: Single Cell Multi-Omics Analysis (MTP)
href: articles/human_brain_tissue_analysis.html
- text: Additional SpaMTP Features
href: articles/SpaMTP_Additional_Features.html
- text: Handling Big Datasets
href: articles/Big_Data.html
- text: Indexed Metabolite Annotation with RaMP 3.0
href: articles/Metabolite_Annotation_Pipeline.html
- text: Pathway Database Integration and Interaction Provenance
href: articles/Pathway_Database_Integration.html
- text: Refining Metabolite Annotations
href: articles/Annotation_Refinement.html
- text: Simulated scMulti-Omics Analysis
href: articles/Single_Cell_MultiOmics.html
reference:
- title: Loading Spatial Metabolic Data into a SpaMTP Seurat Object
desc: Functions that allow the user to load in SM data in different formats
contents:
- LoadSM
- ReadSM_mtx
- Load_METASPACE
- title: Converting Between Data Objects
desc: Functions that allow the user to convert between SpaMTP Seurat Objects and
Cardinal Objects
contents:
- CardinalToSeurat
- ConvertSeuratToCardinal
- title: Binning Spatial Metabolomic Data
desc: Functions that bin m/z values into a lower resolution/wider peak.
contents: BinSpaMTP
- title: Annotating m/z Masses
desc: Functions required for performing and handling m/z annotation using a reference
metabolic database
contents:
- AnnotateSM
- AnnotateMZ
- AdductRules
- MALDIMatrixProfiles
- MALDIMatrixRules
- BuildMZAnnotationIndex
- QueryMZAnnotationIndex
- AnnotationInfo
- print.spamtp_mz_index
- AddCustomMZAnnotations
- AddFMP10Annotations
- SearchAnnotations
- GetMZMetadata
- FindDuplicateAnnotations
- SubsetMZFeatures
- AnnotateBigData
- getRefinedAnnotations
- title: Simplify Annotations
desc: Functions required for simplifying m/z annotation results
contents:
- CalculateAnnotationStatistics
- CalculateSingleAnnotationStatistics
- Pseudo_msms
- CreatePathwayObject
- title: Simplifying Lipid Nomenclature
desc: Function used to simplify lipid names into general lipid categories, classes,
and more
contents: RefineLipids
- title: Analysis of Differentially Expressed Peaks
desc: Functions required for performing pseudo-bulking differential expression analysis
contents: FindAllDEMs
- title: Visualising DEPs Analysis
desc: Functions used to generate a heatmap from DEP results
contents: DEMsHeatmap
- title: Metabolic and Transcriptomic Pathway Analysis
desc: Functions used to perform pathway analysis, both PCA and metabolite/gene set-based
(GSEA)
contents:
- FishersPathwayAnalysis
- FindRegionalPathways
- RunRAMPgeseca
- CreatePathwayAssay
- title: Metabolic and Transcriptomic Pathway Visualisation
desc: Functions used to visualise pathway analysis results
contents:
- VisualisePathways
- PlotRegionalPathways
- PlotPathways
- PlotPathwaysSpatially
- title: Pathway Network Plotting
desc: Functions used to generate network plots for specified patheays
contents: PathwayNetworkPlots
- title: Dimentionality Reduction Analysis
desc: Functions that are used for calculating PCA embeddings and projections based
on SM and/or ST data
contents:
- RunMetabolicPCA
- RunSpatialGraphPCA
- GetKmeanClusters
- title: SpaMTP Metabolic Data Visualisation
desc: Functions that can be used to visualize data from SpaMTP object
contents:
- ImageMZPlot
- ImageMZAnnotationPlot
- SpatialMZPlot
- SpatialMZAnnotationPlot
- Plot3DFeature
- MassIntensityPlot
- DensityMap
- CheckAlignment
- title: Interactive Spatial Binning Visualisation
desc: Interactive plot that displays spatial changes to m/z intensity values based
on changes to bin size.
contents: InteractiveSpatialPlot
- title: Additional SpaMTP Functions
desc: Functions that can be used to find the closest metabolite and bin the expression
of multiple metabolites into one
contents:
- FindNearestMZ
- BinMetabolites
- title: Spatial Analysis of Metabolomic Data
desc: Functions used to identify spatially correlated features (metabolites/genes)
contents:
- FindCorrelatedFeatures
- FindSpatiallyVariableMetabolites
- GetSpatiallyVariableMetabolites
- RowVar
- title: Multi-Omic Data Integration
desc: Functions used to Align, Map and Integrate Spatial Metabolomic and Transcriptomic
data
contents:
- MapSpatialOmics
- ApplySpatialAlignment
- AlignSpatialOmics
- MultiOmicIntegration
- CreateMergedModalityAssay
- title: Adding Image Data
desc: Functions used to align and add an image to a spatial metabolic SpaMTP object.
contents: AddSMImage
- title: ROI Selection
desc: Functions used subset or select specific spatial regions of interest.
contents: SelectROIs
- title: Pre-Processing SpaMTP Metabolic Data
desc: Functions for normalising and visualising the pre-processing of SpaMTP datasets
contents:
- NormalizeSMData
- TMMNormalize
- MZRidgePlot
- MZVlnPlot
- MZBoxPlot
- title: Exporting SpaMTP Data
desc: Function to export SpaMTP data in .mtx, barcodes.csv, features.csv, metadata.csv,
and feature.metadata.csv files
contents: SaveSpaMTPData
- title: Reference Metabolite Datasets
desc: Metabolite datasets used for annotating m/z masses
contents:
- HMDB_db
- Lipidmaps_db
- Chebi_db
- GNPS_db
- filtered_fmp10
- title: Metabolic Pathway Datasets
desc: Various datasets required for pathway analysis
contents:
- adduct_file
- analyte
- analytehaspathway
- chem_props
- pathway
- source_df
- ramp_db_metadata
- title: Pathway Network Datasets
desc: Various datasets required for generated pathway network plots
contents:
- RAMP_hmdb
- RAMP_Reactome
- RAMP_kegg
- RAMP_wikipathway
- reaction_type
- title: Cardinal Wrapper Functions
desc: Functions used to alter Cardinal Objects.
contents: add_ssc_annotation
- title: Additional Worker Functions
desc: Various helper functions used by SpaMTP
contents:
- verbose_message
- subset_SPM
- check_cardinal_version
- title: Utility Functions
- subtitle: Binning Helper Functions
desc: Helper functions for binning m/z intensity spectra for SpaMTP objects
contents:
- BinnedCardinalToSeurat
- spectral_binning
- subtitle: Plotting Helper Functions
desc: Helper functions used for SpaMTP data visualisation
contents:
- bin.mz
- plusminus
- plot_plus_minus
- check_column_type
- pixelPlot
- subtitle: Annotation Helper Functions
desc: Helper functions required for running 'AnnotateSM()'
contents:
- annotateTable
- labels_to_show
- add_backslashes_to_specialfeatures
- check_and_truncate_adduct_vector
- db_adduct_filter
- is_formula_valid
- formula_filter
- calculate_bounds
- ppm_error
- ppm_range_match
- proc_db
- subtitle: METASPACE Loader helper functions
desc: Helper functions required for running 'Load_METASPACE()'
contents:
- metaspace_client
- get_metaspace
- metaspace_to_feature_matrix
- subtitle: Differential Abundance Helper Functions
desc: Helper functions for calculating and plotting differentially expressed metabolites
contents:
- run_pooling
- run_DE
- save_pheatmap_as_pdf
- subtitle: Pathway Analysis Helper Functions
desc: Helper functions used for running pathway analysis
contents:
- PlotSinglePathway
- PlotSinglePathwaySpatially
- addGesecaScores
- get_analytes_db
- list_to_pprcomp
- subtitle: Multi-Omic Helper Functions
desc: Helper functions used in multi-omic analysis functions
contents:
- kneighbors_graph
- get_square_coordinates
- lowresMapping
- hiresMapping
- translate
- mirror
- stretch
- rigid.rot
- rigid.transf
- rigid.transl
- rigid.refl
- rigid.stretch
- combine.tr
- subtitle: Pre-Processing Helper Functions
desc: Helper functions for generating pre-processing plots
contents: statPlot
extra_files:
- vignettes/vignette_data_files/Mouse_Urinary_Bladder/3d_plot1.html
- vignettes/vignette_data_files/Mouse_Urinary_Bladder/3d_plot2.html
- vignettes/vignette_data_files/Mouse_Urinary_Bladder/3d_plot3.html
- vignettes/vignette_data_files/Mouse_Urinary_Bladder/3d_plot4.html
- vignettes/vignette_data_files/Spotted_Liver/SelectROI_Expample.png
search:
exclude: ['news/index.html']
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