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url: https://drieslab.github.io/Giotto_website/
authors:
Ruben Dries:
href: https://www.drieslab.com
Guo-Cheng Yuan:
href: https://labs.icahn.mssm.edu/yuanlab/
Joselyn C. Chávez-Fuentes:
href: https://josschavezf.github.io
template:
includes:
in_header: |
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window.dataLayer = window.dataLayer || [];
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gtag('js', new Date());
gtag('config', 'G-2V1K0KPLJC');
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<link href="extra.css" type="text/css" rel="stylesheet">
bootstrap: 3
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code_font: {google: "JetBrains Mono"}
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structure:
left:
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- reference
- articles
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right:
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get_started:
text: Get started
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- text: Giotto Installation
href: articles/installation.html
- text: Giotto Ecosystem
href: articles/ecosystem.html
- text: Giotto Class Structure
href: articles/structure.html
- text: General Giotto Workflow
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- text: Giotto Core Functions
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- text: FAQs
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- text: How to report a bug
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- text: Create a simulated dataset object
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- text: Create and change Giotto instructions
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- text: -------
- text: Giotto Configuration
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- text: -------
- text: Pre-Processing
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- text: -------
- text: Analysis
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- text: Process Giotto convenience function
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- text: Detection of Highly Variable Features
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- text: Dimension reduction
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- text: Spatial and feature networks
href: articles/networks.html
- text: Finding Differential Expressed Genes
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- text: Deconvolution
href: articles/deconvolution.html
- text: PAGE and Rank Enrichment
href: articles/page_rank_enrichment.html
- text: Kriging
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- text: Tesselation
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- text: -------
- text: Spatial Patterns
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- text: Detection of spatial genes
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- text: Detection of spatial co-expression modules
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- text: Spatially Informed clusters
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- text: Spatial domain analysis using HMRF
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- text: -------
- text: Multiple samples
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- text: Object splitting and joining
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- text: Batch effect removal with Harmony
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- text: Tissue Microarrays
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- text: -------
- text: Spatial manipulation
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- text: Spatial geometries
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- text: -------
- text: Image alignment
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href: articles/image_alignment.html
- text: -------
- text: Interactivity
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- text: Interactive selection
href: articles/interactive_selection.html
- text: Interactive visualization with vitessceR
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- text: Interactive region selection on large datasets
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- text: -------
- text: Visualizations
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- text: Metafeatures
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- text: Cross section
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- text: -------
- text: Saving and Loading
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- text: Saving plots
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- text: -------
- text: Interoperability
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- text: Integrate Bento Analysis
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- text: Integrate ONTraC Analysis
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- text: SpatialExperiment
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- text: Seurat
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- text: SpatialData
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- text: -------
- text: Try Giotto in the Cloud
menu:
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- text: NeMO Slide-seq on Terra.bio
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- text: -------
- text: Containers
menu:
- text: Docker
href: articles/docker.html
- text: Singularity
href: articles/singularity.html
- text: -------
- text: Scalability
menu:
- text: Using dbMatrix with Giotto
href: articles/dbMatrix.html
articles:
text: Examples
menu:
- text: Seq-Scope
menu:
- text: Mouse liver
href: articles/seqscope_mouse_liver.html
- text: -------
- text: Visium
menu:
- text: Visium Mouse Kidney
href: articles/visium_mouse_kidney.html
- text: Visium Mouse Brain
href: articles/visium_mouse_brain.html
- text: Visium Prostate Integration
href: articles/visium_prostate_integration.html
- text: CytAssist Human Lung Cancer
href: articles/visium_cytassist_lungcancer.html
- text: CytAssist Multi-omics Human Glioblastoma
href: articles/visium_cytassist_human_glioblastoma.html
- text: VisiumHD Human Colorectal Cancer
href: articles/VisiumHD_Human_Colorectal_Cancer.html
- text: -------
- text: Slide-seq
menu:
- text: Slide-seq Mouse brain
href: articles/slideseq_mouse_brain.html
- text: -------
- text: Spatial Genomics
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- text: Mouse Kidney
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- text: -------
- text: DBiT-Seq
menu:
- text: Multi-omics Mouse Embryo DBiT-Seq
href: articles/mouse_embryo_dbitseq.html
- text: -------
- text: Spatial CITE-Seq
menu:
- text: Multi-omics Spatial CITE-Seq Human skin
href: articles/spatial_citeseq_human_skin.html
- text: -------
- text: Xenium
menu:
- text: Xenium Human breast cancer
href: articles/xenium_breast_cancer.html
- text: -------
- text: Nanostring CosMx
menu:
- text: Nanostring CosMx Subcellular Lung Cancer
href: articles/nanostring_cosmx_lung_cancer.html
- text: -------
- text: MERFISH
menu:
- text: MERFISH Mouse Hypothalamic Preoptic Region
href: articles/merfish_mouse_hypothalamic.html
- text: -------
- text: Vizgen
menu:
- text: Vizgen Mouse Brain Receptor Map
href: articles/vizgen_mouse_brain.html
- text: -------
- text: Open-ST
menu:
- text: Open-ST Mouse Hippocampus
href: articles/openst_mouse_hippocampus.html
- text: -------
- text: seqFISH
menu:
- text: mini seqFISH
href: articles/mini_seqfish.html
- text: SeqFish+ Mouse Cortex Example
href: articles/seqfish_cortex.html
- text: -------
- text: osmFISH
menu:
- text: osmFISH Mouse SS Cortex
href: articles/osmfish_mouse_ss_cortex.html
- text: -------
- text: Resolve Bioscience
menu:
- text: Resolve Bioscience Breast Cancer Subcellular
href: articles/resolve_biosciences.html
- text: Resolve Bioscience Human lung
href: articles/resolve_biosciences_human_lung.html
- text: -------
- text: CODEX
menu:
- text: Codex Mouse Spleen
href: articles/codex_mouse_spleen.html
- text: -------
- text: Single Cell RNA Sequencing
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- text: Prostate
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- text: Prostate Integration
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- text: Human Lung Adenocarcinoma
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contributing:
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- text: Coding style
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- text: Giotto-specific Dispatch Functions
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- text: Package imports
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- text: Getters and Setters
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- text: Python code
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- text: Contributing tutorials to the website
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news:
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- text: Presentations
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- text: Branches
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- title: Scalability
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reference:
- title: Giotto Environment
desc: Install and work with Giotto Python Environment.
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- GiottoClass::removeGiottoEnvironment
- GiottoClass::checkGiottoEnvironment
- title: Giotto Instructions
desc: Create or change Giotto instructions.
- contents:
- GiottoClass::createGiottoInstructions
- GiottoClass::instructions
- title: Import Raw Data
desc: Functions to help to import raw spatial data.
- contents:
- GiottoData::getSpatialDataset
- GiottoClass::readExprMatrix
- get10Xmatrix
- get10Xmatrix_h5
- GiottoClass::stitchFieldCoordinates
- GiottoClass::stitchTileCoordinates
- readPolygonFilesVizgen
- readPolygonFilesVizgenHDF5
- readPolygonVizgenParquet
- getGEFtxCoords
- title: Images
desc: Functions to work with images for a Giotto object.
- contents:
- GiottoClass::estimateImageBg
- GiottoClass::changeImageBg
- GiottoClass::createGiottoImage
- GiottoClass::addGiottoImage
- GiottoVisuals::addGiottoImageToSpatPlot
- GiottoClass::showGiottoImageNames
- GiottoClass::updateGiottoImage
- GiottoClass::getGiottoImage
- GiottoClass::plotGiottoImage
- GiottoClass::setGiottoImage
- GiottoClass::addGiottoLargeImage
- GiottoClass::createGiottoLargeImage
- GiottoClass::createGiottoLargeImageList
- createMerscopeLargeImage
- GiottoClass::cropGiottoLargeImage
- GiottoClass::updateGiottoLargeImage
- GiottoClass::writeGiottoLargeImage
- GiottoClass::stitchGiottoLargeImage
- GiottoClass::convertGiottoLargeImageToMG
- GiottoClass::addGiottoImageMG
- GiottoClass::updateGiottoImageMG
- GiottoClass::distGiottoImage
- GiottoClass::reconnectGiottoImage
- registerImagesFIJI
- registerGiottoObjectList
- registerGiottoObjectListFiji
- registerGiottoObjectListRvision
- estimateAutomatedImageRegistrationWithSIFT
- .sift_detect
- .warp_transformed_image
- .estimate_transform_from_matched_descriptor
- .match_descriptor
- .plot_matched_descriptors
- preprocessImageToMatrix
- title: Giotto Object
desc: Functions to help to import raw spatial data.
- contents:
- GiottoClass::createGiottoObject
- createGiottoVisiumObject
- createGiottoVisiumHDObject
- GiottoClass::createGiottoObjectSubcellular
- createGiottoCosMxObject
- createGiottoMerscopeObject
- createGiottoObjectfromArchR
- createArchRProj
- createGiottoXeniumObject
- readPolygonFilesVizgenHDF5_old
- importCosMx
- importVisiumHD
- importXenium
- read10xAffineImage
- title: Load and Save Giotto Object
desc: Functions to help loading and saving a giotto object from and to a local folder.
- contents:
- GiottoClass::loadGiotto
- GiottoClass::saveGiotto
- title: Giotto Helper Functions
desc: Common functions to help working with Giotto objects.
- contents:
- GiottoClass::pDataDT
- GiottoClass::fDataDT
- GiottoClass::showProcessingSteps
- GiottoClass::calculateMetaTable
- GiottoClass::calculateMetaTableCells
- GiottoClass::createMetafeats
- findNetworkNeighbors
- GiottoClass::objHistory
- fiji
- title: Report Extractors
desc: Functions to extract report tables of information
- contents:
- GiottoClass::spatValues
- GiottoClass::combineCellData
- GiottoClass::combineFeatureData
- GiottoClass::combineMetadata
- GiottoClass::combineSpatialCellMetadataInfo
- GiottoClass::combineFeatureOverlapData
- title: Giotto Getters & Setters
desc: Low level functions to get, set and show Giotto slots.
- contents:
- GiottoClass::getExpression
- GiottoClass::setExpression
- GiottoClass::getSpatialLocations
- GiottoClass::setSpatialLocations
- GiottoClass::getDimReduction
- GiottoClass::setDimReduction
- GiottoClass::getNearestNetwork
- GiottoClass::setNearestNetwork
- GiottoClass::getSpatialNetwork
- GiottoClass::setSpatialNetwork
- GiottoClass::getSpatialGrid
- GiottoClass::setSpatialGrid
- GiottoClass::getPolygonInfo
- GiottoClass::setPolygonInfo
- GiottoClass::getFeatureInfo
- GiottoClass::setFeatureInfo
- GiottoClass::getFeatureMetadata
- GiottoClass::setFeatureMetadata
- GiottoClass::getSpatialEnrichment
- GiottoClass::setSpatialEnrichment
- GiottoClass::getCellMetadata
- GiottoClass::setCellMetadata
- GiottoClass::getMultiomics
- GiottoClass::setMultiomics
- title: Giotto Show Slots
desc: Show what is available in different information slots.
- contents:
- GiottoClass::showGiottoExpression
- GiottoClass::showGiottoCellMetadata
- GiottoClass::showGiottoDimRed
- GiottoClass::showGiottoFeatInfo
- GiottoClass::showGiottoFeatMetadata
- GiottoClass::showGiottoImageNames
- GiottoClass::showGiottoInstructions
- GiottoClass::showGiottoNearestNetworks
- GiottoClass::showGiottoSpatEnrichments
- GiottoClass::showGiottoSpatGrids
- GiottoClass::showGiottoSpatialInfo
- GiottoClass::showGiottoSpatLocs
- GiottoClass::showGiottoSpatNetworks
- GiottoClass::showGrids
- GiottoClass::showNetworks
- showPattern
- showPattern2D
- showPattern3D
- showPatternGenes
- title: Modify Giotto Object
desc: Modifications to the Giotto objects.
- contents:
- filterGiotto
- filterCombinations
- filterDistributions
- GiottoClass::subsetGiotto
- GiottoClass::subsetGiottoLocs
- GiottoClass::subsetGiottoLocsMulti
- GiottoClass::joinGiottoObjects
- normalizeGiotto
- adjustGiottoMatrix
- GiottoClass::annotateGiotto
- GiottoClass::removeCellAnnotation
- GiottoClass::removeFeatAnnotation
- GiottoClass::addCellMetadata
- GiottoClass::addFeatMetadata
- labelTransfer
- addFeatStatistics
- addCellStatistics
- addStatistics
- addFeatsPerc
- addCellIntMetadata
- processGiotto
- filterCPG
- title: Dimension Reduction
desc: Functions to reduce dimensions.
- contents:
- calculateHVF
- signPCA
- screePlot
- create_screeplot
- jackstrawPlot
- reduceDims
- runNMF
- runPCA
- runUMAP
- runtSNE
- runGiottoHarmony
- runWNN
- runIntegratedUMAP
- runPCAprojection
- runPCAprojectionBatch
- runUMAPprojection
- title: Clustering
desc: Functions to cluster cells.
- contents:
- calculateHVF
- GiottoClass::createNearestNetwork
- GiottoClass::addNetworkLayout
- clusterCells
- doLeidenCluster
- doLeidenClusterIgraph
- doLouvainCluster
- doKmeans
- doHclust
- doRandomWalkCluster
- doSNNCluster
- subClusterCells
- doLeidenSubCluster
- doLouvainSubCluster
- getClusterSimilarity
- mergeClusters
- getDendrogramSplits
- doClusterProjection
- doGiottoClustree
- title: Marker Genes
desc: Functions to detect cell type / cluster specific marker genes.
- contents:
- findMarkers
- findMarkers_one_vs_all
- findGiniMarkers
- findGiniMarkers_one_vs_all
- findScranMarkers
- findScranMarkers_one_vs_all
- findMastMarkers
- findMastMarkers_one_vs_all
- title: Spatial Enrichment
desc: Algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix.
- contents:
- makeSignMatrixPAGE
- makeSignMatrixRank
- runSpatialEnrich
- runPAGEEnrich
- runRankEnrich
- runHyperGeometricEnrich
- createSpatialGenomicsObject
- doFeatureSetEnrichment
- selectPatternGenes
- silhouetteRank
- silhouetteRankTest
- title: Spatial Deconvolution
desc: Algorithms to perform spatial deconvolution based on gene signatures or single-cell RNAseq information.
- contents:
- makeSignMatrixDWLSfromMatrix
- makeSignMatrixDWLS
- runSpatialDeconv
- runDWLSDeconv
- GiottoVisuals::spatDeconvPlot
- featExpDWLS
- title: Spatial Network or Grid
desc: Function to (help) create a spatial network or grid.
- contents:
- GiottoVisuals::spatNetwDistributionsDistance
- GiottoVisuals::spatNetwDistributionsKneighbors
- GiottoVisuals::spatNetwDistributions
- GiottoClass::createSpatialDelaunayNetwork
- GiottoVisuals::plotStatDelaunayNetwork
- GiottoClass::createSpatialKNNnetwork
- GiottoClass::annotateSpatialNetwork
- GiottoClass::annotateSpatialGrid
- GiottoClass::createSpatialGrid
- GiottoClass::createSpatialDefaultGrid
- identifyTMAcores
- title: Spatial Expression Patterns
desc: Methods to detect spatially coherent expression patterns.
- contents:
- binSpectSingleMatrix
- binSpectSingle
- binSpectMultiMatrix
- binSpectMulti
- binSpect
- spatialDE
- spatialAEH
- trendSceek
- spark
- filterSpatialGenes
- title: Simulate Spatial Expression Patterns
desc: Function to simulate a user-defined pattern using the full complexity of the different gene distributions.
- contents:
- simulateOneGenePatternGiottoObject
- runPatternSimulation
- title: Spatial Co-Expression Modules
desc: Method to detect spatially co-expressed feature modules.
- contents:
- clusterSpatialCorFeats
- detectSpatialCorFeats
- clusterSpatialCorGenes
- detectSpatialCorFeatsMatrix
- detectSpatialPatterns
- heatmSpatialCorFeats
- showSpatialCorFeats
- showSpatialCorGenes
- rankSpatialCorGroups
- getBalancedSpatCoexpressionFeats
- title: Hidden Markov Random Field (HMRF)
desc: Functions to identify spatial domains with HMRF.
- contents:
- doHMRF
- doHMRF_V2
- initHMRF_V2
- loadHMRF
- viewHMRFresults
- viewHMRFresults_V2
- writeHMRFresults
- addHMRF
- addHMRF_V2
- viewHMRFresults
- viewHMRFresults2D
- viewHMRFresults3D
- title: Basic Visualizations
desc: Functions for different visualization options to explore gene, cell or cluster characteristics.
- contents:
- GiottoVisuals::showClusterHeatmap()
- GiottoVisuals::showClusterDendrogram
- GiottoVisuals::plotHeatmap
- GiottoVisuals::plotMetaDataHeatmap
- GiottoVisuals::plotMetaDataCellsHeatmap
- GiottoVisuals::violinPlot
- GiottoVisuals::dotPlot
- title: 2D Visualization In Expression Space
desc: Visualization of expression space (e.g. UMAP) in 2D.
- contents:
- GiottoVisuals::dimPlot
- GiottoVisuals::dimPlot2D
- GiottoVisuals::plotUMAP
- GiottoVisuals::plotUMAP_2D
- GiottoVisuals::plotTSNE
- GiottoVisuals::plotTSNE_2D
- GiottoVisuals::plotPCA
- GiottoVisuals::plotPCA_2D
- GiottoVisuals::dimFeatPlot2D
- GiottoVisuals::dimCellPlot2D
- title: 2D Visualization in Spatial Space
desc: Visualization of expression space (e.g. UMAP) in 2D.
- contents:
- GiottoVisuals::spatPlot2D
- GiottoVisuals::spatCellPlot2D
- GiottoVisuals::spatFeatPlot2D
- title: 2D Visualization In Both Spatial And Expression Space
desc: Visualization in both 2D spatial and expression space.
- contents:
- GiottoVisuals::spatDimPlot2D
- GiottoVisuals::spatDimCellPlot2D
- GiottoVisuals::spatDimFeatPlot2D
- title: 3D Visualization Dimension Reduction
desc: Visualization of expression space (e.g. UMAP) in 3D.
- contents:
- GiottoVisuals::dimPlot3D
- GiottoVisuals::plotTSNE_3D
- GiottoVisuals::plotPCA_3D
- title: 3D Visualization In Spatial Space
desc: Visualization in 3D spatial space.
- contents:
- GiottoVisuals::spatPlot3D
- title: 3D visualization in Spatial and Expression Space
desc: Visualization in 3D spatial space.
- contents:
- GiottoVisuals::spatDimPlot3D
- title: Plotting Utilities
desc: Functions to assist in plotting.
- contents:
- GiottoUtils::getDistinctColors
- GiottoUtils::getRainbowColors
- GiottoVisuals::getColors
- GiottoVisuals::showSaveParameters
- title: In Silico Cross Sections
desc: Functions to create an in silico 2D cross sections from 3D data.
- contents:
- createCrossSection
- crossSectionPlot
- crossSectionFeatPlot
- crossSectionPlot3D
- crossSectionFeatPlot3D
- insertCrossSectionSpatPlot3D
- insertCrossSectionFeatPlot3D
- create_crossSection_object
- title: Cell Neighborhood, Cell-Type/Cell-Type Enrichment
desc: Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
- contents:
- cellProximityEnrichment
- cellProximityEnrichmentEachSpot
- cellProximityEnrichmentSpots
- cellProximityBarplot
- cellProximityHeatmap
- cellProximityNetwork
- cellProximitySpatPlot
- cellProximitySpatPlot3D
- specificCellCellcommunicationScores
- filterCellProximityGenes
- findCellProximityGenes
- findCellTypesFromEnrichment
- pieCellTypesFromEnrichment
- plotCellTypesFromEnrichment
- plotCellProximityFeatSpot
- showCellProportionSwitchedPie
- showCellProportionSwitchedSanKey
- spatCellCellcomSpots
- title: Cell Neighborhood, Spatial Interaction Changed Features (ICF)
desc: Identify and visualize features (genes) that change in a source cell type due to interaction with another neighboring cell type.
- contents:
- findInteractionChangedFeats
- findICF
- findICFSpot
- findICG
- findCPG
- filterInteractionChangedFeats
- filterInteractionChangedGenes
- filterICF
- filterICFSpot
- filterICG
- plotICF
- plotICFSpot
- plotCellProximityFeats
- plotCPF
- combineInteractionChangedFeats
- combineICF
- plotCombineInteractionChangedFeats
- plotInteractionChangedFeats
- plotCombineICF
- combineCPG
- combineCellProximityGenes
- combineICG
- combineInteractionChangedGenes
- findInteractionChangedGenes
- spatialAutoCor
- spdepAutoCorr
- spatialSplitCluster
- title: Cell Neighborhood, Ligand-Receptor Cell Communication
desc: Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
- contents:
- combCCcom
- exprCellCellcom
- spatCellCellcom
- plotCCcomDotplot
- plotRankSpatvsExpr
- plotRecovery
- plotCCcomHeatmap
- plotCombineCellCellCommunication
- plotCombineCCcom
- title: Subcellular
desc: Functions to manipulate and visualize subcellular data.
- contents:
- addPolygonCells
- GiottoClass::addGiottoPoints
- GiottoClass::addGiottoPoints3D
- GiottoClass::addGiottoPolygons
- addVisiumPolygons
- GiottoClass::addSpatialCentroidLocations
- GiottoClass::addSpatialCentroidLocationsLayer
- GiottoClass::calculateOverlapParallel
- GiottoClass::calculateOverlapPolygonImages
- GiottoClass::calculateOverlapRaster
- GiottoClass::calculateOverlapSerial