Package index • Giotto

Giotto Environment Install and work with Giotto Python Environment.
`checkGiottoEnvironment()` `installGiottoEnvironment()` `removeGiottoEnvironment()` `set_giotto_python_path()`	Giotto python environment (from GiottoClass)
`checkGiottoEnvironment()` `installGiottoEnvironment()` `removeGiottoEnvironment()` `set_giotto_python_path()`	Giotto python environment (from GiottoClass)
`checkGiottoEnvironment()` `installGiottoEnvironment()` `removeGiottoEnvironment()` `set_giotto_python_path()`	Giotto python environment (from GiottoClass)
Giotto Instructions Create or change Giotto instructions.
`createGiottoInstructions()` `instructions(<missing>,<missing>)` `instructions(<giotto>,<missing>)` `instructions(<giotto>,<character>)` `instructions(<giottoInstructions>,<character>)` `instructions<-`(<giotto>,<missing>,<missing>) `instructions<-`(<giotto>,<missing>,<logical>) `instructions<-`(<giotto>,<character>,<missing>) `instructions<-`(<giotto>,<character>,<logical>) `instructions<-`(<giottoInstructions>,<character>,<ANY>)	Giotto instructions (from GiottoClass)
`createGiottoInstructions()` `instructions(<missing>,<missing>)` `instructions(<giotto>,<missing>)` `instructions(<giotto>,<character>)` `instructions(<giottoInstructions>,<character>)` `instructions<-`(<giotto>,<missing>,<missing>) `instructions<-`(<giotto>,<missing>,<logical>) `instructions<-`(<giotto>,<character>,<missing>) `instructions<-`(<giotto>,<character>,<logical>) `instructions<-`(<giottoInstructions>,<character>,<ANY>)	Giotto instructions (from GiottoClass)
Import Raw Data Functions to help to import raw spatial data.
`getSpatialDataset()`	getSpatialDataset (from GiottoData)
`readExprMatrix()`	Read expression matrix (from GiottoClass)
`get10Xmatrix()`	get10Xmatrix
`get10Xmatrix_h5()`	get10Xmatrix_h5
`stitchFieldCoordinates()`	stitchFieldCoordinates (from GiottoClass)
`stitchTileCoordinates()`	stitchTileCoordinates (from GiottoClass)
`readPolygonFilesVizgen()` `.h5_read_vizgen()`	readPolygonFilesVizgen
`readPolygonFilesVizgenHDF5()`	readPolygonFilesVizgenHDF5
`readPolygonVizgenParquet()`	Read MERSCOPE polygons from parquet
`getGEFtxCoords()`	getGEFtxCoords
Images Functions to work with images for a Giotto object.
`estimateImageBg()`	estimateImageBg (from GiottoClass)
`changeImageBg()`	changeImageBg (from GiottoClass)
`createGiottoImage()`	createGiottoImage (from GiottoClass)
`addGiottoImage()`	addGiottoImage (from GiottoClass)
`addGiottoImageToSpatPlot()`	addGiottoImageToSpatPlot (from GiottoVisuals)
`showGiottoImageNames()`	showGiottoImageNames (from GiottoClass)
`updateGiottoImage()`	updateGiottoImage (from GiottoClass)
`getGiottoImage()`	Get giotto image object (from GiottoClass)
`plotGiottoImage()`	Plot a giotto image object (from GiottoClass)
`setGiottoImage()`	Set giotto image object (from GiottoClass)
`addGiottoLargeImage()`	addGiottoLargeImage (from GiottoClass)
`createGiottoLargeImage()`	createGiottoLargeImage (from GiottoClass)
`createGiottoLargeImageList()`	createGiottoLargeImageList (from GiottoClass)
`createMerscopeLargeImage()`	Create Vizgen MERSCOPE largeImage
`cropGiottoLargeImage()`	Crop a giotto largeImage object (from GiottoClass)
`updateGiottoLargeImage()`	updateGiottoLargeImage (from GiottoClass)
`writeGiottoLargeImage()`	writeGiottoLargeImage (from GiottoClass)
`stitchGiottoLargeImage()`	Stitch multiple giottoLargeImage objects into a single giottoLargeImage object (from GiottoClass)
`convertGiottoLargeImageToMG()`	convertGiottoLargeImageToMG (from GiottoClass)
`addGiottoImageMG()`	addGiottoImageMG (from GiottoClass)
`updateGiottoImageMG()`	updateGiottoImageMG (from GiottoClass)
`distGiottoImage()`	Plot distribution of image intensity values (from GiottoClass)
`reconnectGiottoImage()`	Reconnect images with dead pointers (from GiottoClass)
`registerImagesFIJI()`	registerImagesFIJI
`registerGiottoObjectList()`	registerGiottoObjectList
`registerGiottoObjectListFiji()`	registerGiottoObjectListFiji
`registerGiottoObjectListRvision()`	registerGiottoObjectListRvision
`estimateAutomatedImageRegistrationWithSIFT()`	Estimate Automated ImageRegistration With SIFT
`.sift_detect()`	Run SIFT feature detector and descriptor extractor
`.warp_transformed_image()`	Warp transformed images from estimated transformation
`.estimate_transform_from_matched_descriptor()`	Estimate affine transformation from matched descriptor
`.match_descriptor()`	Match image descriptors
`.plot_matched_descriptors()`	plot matched descriptors
`preprocessImageToMatrix()`	Preprocess from image directory to the required matrix format for Image registration pipeline built on scikit-image
Giotto Object Functions to help to import raw spatial data.
`createGiottoObject()`	Create a giotto object (from GiottoClass)
`createGiottoVisiumObject()`	Create a giotto object from 10x visium data
`createGiottoVisiumHDObject()`	Create 10x VisiumHD Giotto Object
`createGiottoObjectSubcellular()`	Create a giotto object from subcellular data (from GiottoClass)
`createGiottoCosMxObject()`	Create Nanostring CosMx Giotto Object
`createGiottoMerscopeObject()` `.createGiottoMerscopeObject_subcellular()` `.createGiottoMerscopeObject_aggregate()`	Create Vizgen MERSCOPE Giotto Object
`createGiottoObjectfromArchR()`	Create a Giotto object from an ArchR project
`createArchRProj()`	Create an ArchR project and run LSI dimension reduction
`createGiottoXeniumObject()`	Create 10x Xenium Giotto Object
`readPolygonFilesVizgenHDF5_old()`	readPolygonFilesVizgenHDF5
`importCosMx()`	Import a Nanostring CosMx Assay
`importVisiumHD()`	Import a Visium HD assay
`importXenium()`	Import a 10X Xenium Assay
`read10xAffineImage()`	read10xAffineImage
Load and Save Giotto Object Functions to help loading and saving a giotto object from and to a local folder.
`loadGiotto()`	loadGiotto (from GiottoClass)
`saveGiotto()`	saveGiotto (from GiottoClass)
Giotto Helper Functions Common functions to help working with Giotto objects.
`pDataDT()`	pDataDT (from GiottoClass)
`fDataDT()`	fDataDT (from GiottoClass)
`showProcessingSteps()`	showProcessingSteps (from GiottoClass)
`calculateMetaTable()`	calculateMetaTable (from GiottoClass)
`calculateMetaTableCells()`	calculateMetaTableCells (from GiottoClass)
`combineMetadata()`	combineMetadata (from GiottoClass)
`createMetafeats()`	createMetafeats (from GiottoClass)
`findNetworkNeighbors()`	Find network neighbors
`objHistory()`	Giotto object history (from GiottoClass)
`fiji()`	Find Fiji location
Giotto Getters & Setters Low level functions to get, set and show Giotto slots.
`getExpression()`	Get expression values (from GiottoClass)
`setExpression()`	Set expression data (from GiottoClass)
`getSpatialLocations()`	Get spatial locations (from GiottoClass)
`setSpatialLocations()`	Set spatial locations (from GiottoClass)
`getDimReduction()`	Get dimension reduction (from GiottoClass)
`setDimReduction()`	Set dimension reduction data (from GiottoClass)
`getNearestNetwork()`	Get nearest neighbor network (from GiottoClass)
`setNearestNetwork()`	Set nearest neighbor network (from GiottoClass)
`getSpatialNetwork()`	Get spatial network (from GiottoClass)
`setSpatialNetwork()`	Set spatial network (from GiottoClass)
`getSpatialGrid()`	Get spatial grid (from GiottoClass)
`setSpatialGrid()`	Set spatial grid (from GiottoClass)
`getPolygonInfo()`	Get polygon info (from GiottoClass)
`setPolygonInfo()`	Set polygon info (from GiottoClass)
`getFeatureInfo()`	Get feature info (from GiottoClass)
`setFeatureInfo()`	Set feature info (from GiottoClass)
`getFeatureMetadata()`	getFeatureMetadata (from GiottoClass)
`setFeatureMetadata()`	Set feature metadata (from GiottoClass)
`getSpatialEnrichment()`	Get spatial enrichment (from GiottoClass)
`setSpatialEnrichment()`	Set spatial enrichment (from GiottoClass)
`getCellMetadata()`	getCellMetadata (from GiottoClass)
`setCellMetadata()`	Set cell metadata (from GiottoClass)
`getMultiomics()`	Get multiomics integration results (from GiottoClass)
`setMultiomics()`	Set multiomics integration results (from GiottoClass)
Giotto Show Slots Show what is available in different information slots.
`showGiottoExpression()`	showGiottoExpression (from GiottoClass)
`showGiottoCellMetadata()`	showGiottoCellMetadata (from GiottoClass)
`showGiottoDimRed()`	showGiottoDimRed (from GiottoClass)
`showGiottoFeatInfo()`	showGiottoFeatInfo (from GiottoClass)
`showGiottoFeatMetadata()`	showGiottoFeatMetadata (from GiottoClass)
`showGiottoImageNames()`	showGiottoImageNames (from GiottoClass)
`showGiottoInstructions()`	deprecated (from GiottoClass)
`showGiottoNearestNetworks()`	showGiottoNearestNetworks (from GiottoClass)
`showGiottoSpatEnrichments()`	showGiottoSpatEnrichments (from GiottoClass)
`showGiottoSpatGrids()`	showGiottoSpatGrids (from GiottoClass)
`showGiottoSpatialInfo()`	showGiottoSpatialInfo (from GiottoClass)
`showGiottoSpatLocs()`	showGiottoSpatLocs (from GiottoClass)
`showGiottoSpatNetworks()`	showGiottoSpatNetworks (from GiottoClass)
`showGrids()`	Show Spatial Grids (from GiottoClass)
`showNetworks()`	Show networks (from GiottoClass)
`showPattern()`	showPattern
`showPattern2D()`	showPattern2D
`showPattern3D()`	showPattern3D
`showPatternGenes()`	showPatternGenes
Modify Giotto Object Modifications to the Giotto objects.
`filterGiotto()`	filterGiotto
`filterCombinations()`	filterCombinations
`filterDistributions()`	filterDistributions
`subsetGiotto()`	subsetGiotto (from GiottoClass)
`subsetGiottoLocs()`	Subset by spatial locations (from GiottoClass)
`subsetGiottoLocsMulti()`	deprecated (from GiottoClass)
`joinGiottoObjects()`	Join giotto objects (from GiottoClass)
`normalizeGiotto()`	normalizeGiotto
`adjustGiottoMatrix()`	Adjust expression values
`annotateGiotto()`	Annotate Giotto object (from GiottoClass)
`removeCellAnnotation()`	Remove cell annotation (from GiottoClass)
`removeFeatAnnotation()`	Remove feature annotation (from GiottoClass)
`addCellMetadata()`	Add cell metadata (from GiottoClass)
`addFeatMetadata()`	Add feature metadata (from GiottoClass)
`labelTransfer(<giotto>,<giotto>)` `labelTransfer(<giotto>,<missing>)`	Transfer labels/annotations between sets of data via similarity voting
`addFeatStatistics()`	Add feature statistics
`addCellStatistics()`	addCellStatistics
`addStatistics()`	addStatistics
`addFeatsPerc()`	addFeatsPerc
`addCellIntMetadata()`	addCellIntMetadata
`processGiotto()`	processGiotto
`filterCPG()`	deprecated
Dimension Reduction Functions to reduce dimensions.
`calculateHVF()`	calculateHVF
`signPCA()`	signPCA
`screePlot()`	screePlot
`create_screeplot()`	create_screeplot
`jackstrawPlot()`	jackstrawPlot
`reduceDims()`	Run dimension reduction method
`runNMF()`	Run Non-Negative Matrix Factorization
`runPCA()`	runPCA
`runUMAP()`	Run UMAP dimension reduction
`runtSNE()`	Run tSNE dimensional reduction
`runGiottoHarmony()`	runGiottoHarmony
`runWNN()`	Multi omics integration with WNN
`runIntegratedUMAP()`	Run integrated UMAP
`runPCAprojection()`	runPCAprojection
`runPCAprojectionBatch()`	runPCAprojectionBatch
`runUMAPprojection()`	Run UMAP dimension reduction
Clustering Functions to cluster cells.
`calculateHVF()`	calculateHVF
`createNearestNetwork()`	createNearestNetwork (from GiottoClass)
`addNetworkLayout()`	addNetworkLayout (from GiottoClass)
`clusterCells()`	clusterCells
`doLeidenCluster()`	doLeidenCluster
`doLeidenClusterIgraph()`	doLeidenClusterIgraph
`doLouvainCluster()`	doLouvainCluster
`doKmeans()`	doKmeans
`doHclust()`	doHclust
`doRandomWalkCluster()`	doRandomWalkCluster
`doSNNCluster()`	doSNNCluster
`subClusterCells()` `doLeidenSubCluster()` `doLouvainSubCluster()`	Cell subclustering
`getClusterSimilarity()`	getClusterSimilarity
`mergeClusters()`	mergeClusters
`getDendrogramSplits()`	getDendrogramSplits
`doClusterProjection()`	Projection of cluster labels
`doGiottoClustree()`	doGiottoClustree
Marker Genes Functions to detect cell type / cluster specific marker genes.
`findMarkers()`	findMarkers
`findMarkers_one_vs_all()`	findMarkers_one_vs_all
`findGiniMarkers()`	findGiniMarkers
`findGiniMarkers_one_vs_all()`	findGiniMarkers_one_vs_all
`findScranMarkers()`	findScranMarkers
`findScranMarkers_one_vs_all()`	findScranMarkers_one_vs_all
`findMastMarkers()`	findMastMarkers
`findMastMarkers_one_vs_all()`	findMastMarkers_one_vs_all
Auxiliary Visualizations Functions for different visualization options to explore gene, cell or cluster characteristics.
`showClusterHeatmap()`	showClusterHeatmap (from GiottoVisuals)
`showClusterDendrogram()`	showClusterDendrogram (from GiottoVisuals)
`plotHeatmap()`	plotHeatmap (from GiottoVisuals)
`plotMetaDataHeatmap()`	plotMetaDataHeatmap (from GiottoVisuals)
`plotMetaDataCellsHeatmap()`	plotMetaDataCellsHeatmap (from GiottoVisuals)
`violinPlot()`	violinPlot (from GiottoVisuals)
`callSpdep()`	Call the spdep function with required parameters
Spatial Enrichment Algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix.
`makeSignMatrixPAGE()` `runPAGEEnrich()`	PAGE feature enrichment
`makeSignMatrixRank()`	makeSignMatrixRank
`runSpatialEnrich()`	runSpatialEnrich
`runRankEnrich()`	runRankEnrich
`runHyperGeometricEnrich()`	runHyperGeometricEnrich
`createSpatialGenomicsObject()`	Create Spatial Genomics Giotto Object
`doFeatureSetEnrichment()`	doFeatureSetEnrichment
`selectPatternGenes()`	selectPatternGenes
`silhouetteRank()`	silhouetteRank
`silhouetteRankTest()`	silhouetteRankTest
Spatial Deconvolution Algorithms to perform spatial deconvolution based on gene signatures or single-cell RNAseq information.
`makeSignMatrixDWLSfromMatrix()`	makeSignMatrixDWLSfromMatrix
`makeSignMatrixDWLS()`	makeSignMatrixDWLS
`runSpatialDeconv()`	runSpatialDeconv
`runDWLSDeconv()`	runDWLSDeconv
`spatDeconvPlot()`	spatDeconvPlot (from GiottoVisuals)
`featExpDWLS()`	featExpDWLS
Spatial Network or Grid Function to (help) create a spatial network or grid.
`spatNetwDistributionsDistance()`	Plot spatial distance distribution (from GiottoVisuals)
`spatNetwDistributionsKneighbors()`	spatNetwDistributionsKneighbors (from GiottoVisuals)
`spatNetwDistributions()`	spatNetwDistributions (from GiottoVisuals)
`createSpatialDelaunayNetwork()`	Create a spatial Delaunay network (from GiottoClass)
`plotStatDelaunayNetwork()`	plotStatDelaunayNetwork (from GiottoVisuals)
`createSpatialKNNnetwork()`	createSpatialKNNnetwork (from GiottoClass)
`annotateSpatialNetwork()`	annotateSpatialNetwork (from GiottoClass)
`annotateSpatialGrid()`	annotateSpatialGrid (from GiottoClass)
`createSpatialGrid()`	createSpatialGrid (from GiottoClass)
`createSpatialDefaultGrid()`	createSpatialDefaultGrid (from GiottoClass)
`identifyTMAcores()`	Split cluster annotations based on a spatial network
Spatial Expression Patterns Methods to detect spatially coherent expression patterns.
`binSpect()` `binSpectSingleMatrix()` `binSpectSingle()` `binSpectMulti()`	binSpect
`binSpectMultiMatrix()`	binSpectMultiMatrix
`spatialDE()`	spatialDE
`spatialAEH()`	spatialAEH
`trendSceek()`	trendSceek
`spark()`	spark
`filterSpatialGenes()`	filterSpatialGenes
Simulate Spatial Expression Patterns Function to simulate a user-defined pattern using the full complexity of the different gene distributions.
`simulateOneGenePatternGiottoObject()`	simulateOneGenePatternGiottoObject
`runPatternSimulation()`	runPatternSimulation
Spatial Co-Expression Modules Method to detect spatially co-expressed feature modules.
`clusterSpatialCorFeats()`	clusterSpatialCorFeats
`detectSpatialCorFeats()` `detectSpatialCorFeatsMatrix()`	Detect spatially correlated features
`clusterSpatialCorGenes()`	clusterSpatialCorGenes
`detectSpatialPatterns()`	detectSpatialPatterns
`heatmSpatialCorFeats()`	heatmSpatialCorFeats
`showSpatialCorFeats()`	showSpatialCorFeats
`showSpatialCorGenes()`	showSpatialCorGenes
`rankSpatialCorGroups()`	rankSpatialCorGroups
`getBalancedSpatCoexpressionFeats()`	Get balanced spatial coexpression features
Spatial Data Handling Functions to condense spatial data.
`combineSpatialCellMetadataInfo()`	combineSpatialCellMetadataInfo (from GiottoClass)
Hidden Markov Random Field (HMRF) Functions to identify spatial domains with HMRF.
`doHMRF()`	doHMRF
`doHMRF_V2()`	doHMRF_V2
`initHMRF_V2()`	initHMRF_V2
`loadHMRF()`	loadHMRF
`viewHMRFresults()`	viewHMRFresults
`viewHMRFresults_V2()`	viewHMRFresults_V2
`writeHMRFresults()`	writeHMRFresults
`addHMRF()`	addHMRF
`addHMRF_V2()`	addHMRF_V2
`viewHMRFresults2D()`	viewHMRFresults2D
`viewHMRFresults3D()`	viewHMRFresults3D
General Plotting Functions to assist in plotting.
	Objects exported from other packages (from GiottoVisuals)
`showSaveParameters()`	showSaveParameters (from GiottoVisuals)
2D Visualization In Expression Space Visualization of expression space (e.g. UMAP) in 2D.
`dimPlot2D()` `dimPlot()` `dimPlot3D()`	Plot dimension reduction (from GiottoVisuals)
`dimPlot2D()` `dimPlot()` `dimPlot3D()`	Plot dimension reduction (from GiottoVisuals)
`plotUMAP()`	plotUMAP (from GiottoVisuals)
`plotUMAP_2D()`	plotUMAP_2D (from GiottoVisuals)
`plotTSNE()`	plotTSNE (from GiottoVisuals)
`plotTSNE_2D()`	plotTSNE_2D (from GiottoVisuals)
`plotPCA()`	plotPCA (from GiottoVisuals)
`plotPCA_2D()`	plotPCA_2D (from GiottoVisuals)
`dimFeatPlot2D()`	dimFeatPlot2D (from GiottoVisuals)
`dimCellPlot2D()` `dimCellPlot()`	dimCellPlot (from GiottoVisuals)
2D Visualization in Spatial Space Visualization of expression space (e.g. UMAP) in 2D.
`spatPlot2D()` `spatPlot()` `spatPlot3D()`	spatPlot (from GiottoVisuals)
`spatCellPlot2D()` `spatCellPlot()`	spatCellPlot (from GiottoVisuals)
`spatFeatPlot2D()`	Plot data in physical space 2D (from GiottoVisuals)
2D Visualization In Both Spatial And Expression Space Visualization in both 2D spatial and expression space.
`spatDimPlot2D()` `spatDimPlot()`	spatDimPlot (from GiottoVisuals)
`spatDimCellPlot2D()`	spatDimCellPlot2D (from GiottoVisuals)
`spatDimFeatPlot2D()`	spatDimFeatPlot2D (from GiottoVisuals)
3D Visualization Dimension Reduction Visualization of expression space (e.g. UMAP) in 3D.
`dimPlot2D()` `dimPlot()` `dimPlot3D()`	Plot dimension reduction (from GiottoVisuals)
`plotTSNE_3D()`	plotTSNE_3D (from GiottoVisuals)
`plotPCA_3D()`	plotPCA_3D (from GiottoVisuals)
3D Visualization In Spatial Space Visualization in 3D spatial space.
`spatPlot2D()` `spatPlot()` `spatPlot3D()`	spatPlot (from GiottoVisuals)
3D visualization in Spatial and Expression Space Visualization in 3D spatial space.
`spatDimPlot3D()`	spatDimPlot3D (from GiottoVisuals)
In Silico Cross Sections Functions to create an in silico 2D cross sections from 3D data.
`createCrossSection()`	createCrossSection
`crossSectionPlot()`	crossSectionPlot
`crossSectionFeatPlot()`	crossSectionFeatPlot
`crossSectionPlot3D()`	crossSectionPlot3D
`crossSectionFeatPlot3D()`	crossSectionFeatPlot3D
`insertCrossSectionSpatPlot3D()`	insertCrossSectionSpatPlot3D
`insertCrossSectionFeatPlot3D()`	insertCrossSectionFeatPlot3D
`create_crossSection_object()`	create_crossSection_object
Cell Neighborhood, Cell-Type/Cell-Type Enrichment Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
`cellProximityEnrichment()`	cellProximityEnrichment
`cellProximityEnrichmentEachSpot()`	cellProximityEnrichmentEachSpot
`cellProximityEnrichmentSpots()`	cellProximityEnrichmentSpots
`cellProximityBarplot()`	cellProximityBarplot
`cellProximityHeatmap()`	cellProximityHeatmap
`cellProximityNetwork()`	cellProximityNetwork
`cellProximitySpatPlot()`	cellProximitySpatPlot
`cellProximitySpatPlot3D()`	cellProximitySpatPlot3D
`spatCellCellcom()` `specificCellCellcommunicationScores()`	Spatial cell cell communication scoring
`filterCellProximityGenes()`	deprecated
`findCellProximityGenes()`	deprecated
`findCellTypesFromEnrichment()`	findCellTypesFromEnrichment
`pieCellTypesFromEnrichment()`	pieCellTypesFromEnrichment
`plotCellTypesFromEnrichment()`	plotCellTypesFromEnrichment
`plotCellProximityFeatSpot()`	plotCellProximityFeatSpot
`showCellProportionSwitchedPie()`	showCellProportionSwitchedPie
`showCellProportionSwitchedSanKey()`	showCellProportionSwitchedSanKey
`spatCellCellcomSpots()`	spatCellCellcomSpots
Cell Neighborhood, Spatial Interaction Changed Features (ICF) Identify and visualize features (genes) that change in a source cell type due to interaction with another neighboring cell type.
`findInteractionChangedFeats()` `findICF()`	findInteractionChangedFeats
`findICFSpot()`	findICFSpot
`findICG()`	deprecated
`findCPG()`	deprecated
`filterInteractionChangedFeats()` `filterICF()`	filterInteractionChangedFeats
`filterInteractionChangedGenes()`	deprecated
`filterICFSpot()`	filterICFSpot
`filterICG()`	deprecated
`plotICF()`	Plot interaction changed features
`plotICFSpot()`	plotICFSpot
`plotCellProximityFeats()`	plotCellProximityFeats
`plotCPF()`	plotCPF
`combineInteractionChangedFeats()` `combineICF()`	combineInteractionChangedFeats
`plotCombineInteractionChangedFeats()`	plotCombineInteractionChangedFeats
`plotInteractionChangedFeats()`	Plot interaction changed features
`plotCombineICF()`	plotCombineICF
`combineCPG()`	deprecated
`combineCellProximityGenes()`	deprecated
`combineICG()`	deprecated
`combineInteractionChangedGenes()`	deprecated
`findInteractionChangedGenes()`	deprecated
`spatialAutoCorGlobal()` `spatialAutoCorLocal()`	Spatial autocorrelation
`spdepAutoCorr()`	Compute spatial auto correlation using spdep
`spatialSplitCluster()`	Split cluster annotations based on a spatial network
Cell Neighborhood, Ligand-Receptor Cell Communication Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.
`combCCcom()`	Combine cell cell communication tables
`exprCellCellcom()`	exprCellCellcom
`spatCellCellcom()` `specificCellCellcommunicationScores()`	Spatial cell cell communication scoring
`plotCCcomDotplot()`	plotCCcomDotplot
`plotRankSpatvsExpr()`	plotRankSpatvsExpr
`plotRecovery()`	plotRecovery
`plotCCcomHeatmap()`	plotCCcomHeatmap
`plotCombineCellCellCommunication()`	plotCombineCellCellCommunication
`plotCombineCCcom()`	plotCombineCCcom
Subcellular Functions to manipulate and visualize subcellular data.
`addPolygonCells()`	Add corresponding polygon IDs to cell metadata
`addGiottoPoints()` `addGiottoPoints3D()`	Add subcellular giotto points object to giotto object (from GiottoClass)
`addGiottoPoints()` `addGiottoPoints3D()`	Add subcellular giotto points object to giotto object (from GiottoClass)
`addGiottoPolygons()`	Add giotto polygons to giotto object (from GiottoClass)
`addVisiumPolygons()`	Add Visium Polygons to Giotto Object
`addSpatialCentroidLocations()`	addSpatialCentroidLocations (from GiottoClass)
`addSpatialCentroidLocationsLayer()`	addSpatialCentroidLocationsLayer (from GiottoClass)
`calculateOverlapParallel()`	calculateOverlapParallel (from GiottoClass)
`calculateOverlapPolygonImages()`	calculateOverlapPolygonImages (from GiottoClass)
`calculateOverlapRaster()`	calculateOverlapRaster (from GiottoClass)
`calculateOverlapSerial()`	calculateOverlapSerial (from GiottoClass)
`combineCellData()`	combineCellData (from GiottoClass)
`combineFeatureData()`	combineFeatureData (from GiottoClass)
`combineFeatureOverlapData()`	combineFeatureOverlapData (from GiottoClass)
`createGiottoPoints(<SpatVector>)` `createGiottoPoints(<data.frame>)`	Create giotto points object (from GiottoClass)
`createGiottoPolygon(<character>)` `createGiottoPolygon(<SpatVector>)` `createGiottoPolygon(<SpatRaster>)` `createGiottoPolygon(<data.frame>)` `createGiottoPolygonsFromMask()` `createGiottoPolygonsFromDfr()` `createGiottoPolygonsFromGeoJSON()`	Create giotto polygons object (from GiottoClass)
`overlapToMatrix(<giotto>)` `overlapToMatrix(<giottoPolygon>)` `overlapToMatrix(<SpatVector>)` `overlapToMatrix(<data.table>)`	overlapToMatrix (from GiottoClass)
`overlapImagesToMatrix()`	overlapImagesToMatrix (from GiottoClass)
`overlapToMatrixMultiPoly()`	overlapToMatrixMultiPoly (from GiottoClass)
`smoothGiottoPolygons()`	smoothGiottoPolygons (from GiottoClass)
`spatInSituPlotDensity()`	spatInSituPlotDensity (from GiottoVisuals)
`spatInSituPlotHex()`	spatInSituPlotHex (from GiottoVisuals)
`spatInSituPlotPoints()`	spatInSituPlotPoints (from GiottoVisuals)
`showPolygonSizeInfluence()`	showPolygonSizeInfluence
Segmentation Function to segment cells in-tissue.
`doCellSegmentation()`	doCellSegmentation
`doCellposeSegmentation()`	perform cellpose segmentation
`calculateAffineMatrixFromLandmarks()`	Calculate a affine transformation matrix from two set of landmarks
Doublet Detection Function to detect doublets in raw expression data.
`doScrubletDetect()`	doScrubletDetect
Interactive Visualizations
`cellProximitySpatPlot2D()`	cellProximitySpatPlot2D
`cellProximityVisPlot()`	cellProximityVisPlot
`comparePolygonExpression()`	Compare gene expression between polygon areas
`getCellsFromPolygon()`	Get cells located within the polygons area
`plotInteractivePolygons()`	Select image regions by plotting interactive polygons
`plotPolygons()`	Plot stored polygons
`plotInteractive3D()`	Plot interactive 3D spatial plot
`compareCellAbundance()`	Compare cell types percent per polygon
`exportGiottoViewer()`	exportGiottoViewer
`interactiveLandmarkSelection()`	title Record landmarks by interactive selection
Interoperability Convert other type of objects into a Giotto object and vice versa.
`seuratToGiotto()`	Deprecated (from GiottoClass)
`giottoToSeurat()`	Deprecated (from GiottoClass)
`giottoToSpatialExperiment()`	Utility function to convert a Giotto object to a SpatialExperiment object. (from GiottoClass)
`giottoToAnnData()`	Convert Giotto to anndata (from GiottoClass)
`giottoToAnndataZarr()`	Create a local anndata zarr folder
`anndataToGiotto()`	Convert anndata to Giotto (from GiottoClass)
`giottoMasterToSuite()`	Convert a master Giotto object to suite (from GiottoClass)
`convertEnsemblToGeneSymbol()`	convertEnsemblToGeneSymbol
Kriging
`interpolateFeature(<giotto>,<missing>)` `interpolateFeature(<spatLocsObj>,<data.frame>)`	Spatial feature interpolation
ONTraC integration Functions to interact with ONTraC.
`installGiottoONTraCEnvironment()`	installGiottoONTraCEnvironment
`runONTraCV1()`	runONTraCV1
`getONTraCv1Input()`	getONTraCv1Input
`loadOntraCResults()`	loadOntraCResults
`load_cell_NT_score()`	load_cell_NT_score
`load_cell_niche_cluster_prob()`	load_cell_niche_cluster_prob
`load_niche_cluster_nt_score()`	load_niche_cluster_nt_score
`cal_cell_niche_cluster_bin()`	cal_cell_niche_cluster_bin
`load_nc_connectivity()`	load_nc_connectivity
`plotCTCompositionInNicheCluster()`	plotCTCompositionInNicheCluster
`plotCellTypeNTScore()`	plotCellTypeNTScore
`plotSpatNicheClusterBin()`	plotSpatNicheClusterBin
`plotSpatNicheClusterProb()`	plotSpatNicheClusterProb
`plotNicheClusterConnectivity()`	plotNicheClusterConnectivity
AI technologies
`writeChatGPTqueryDEG()`	writeChatGPTqueryDEG

Reference

Giotto Environment

Giotto Instructions

Import Raw Data

Images

Giotto Object

Load and Save Giotto Object

Giotto Helper Functions

Giotto Getters & Setters

Giotto Show Slots

Modify Giotto Object

Dimension Reduction

Clustering

Marker Genes

Auxiliary Visualizations

Spatial Enrichment

Spatial Deconvolution

Spatial Network or Grid

Spatial Expression Patterns

Simulate Spatial Expression Patterns

Spatial Co-Expression Modules

Spatial Data Handling

Hidden Markov Random Field (HMRF)

General Plotting

2D Visualization In Expression Space

2D Visualization in Spatial Space

2D Visualization In Both Spatial And Expression Space

3D Visualization Dimension Reduction

3D Visualization In Spatial Space

3D visualization in Spatial and Expression Space

In Silico Cross Sections

Cell Neighborhood, Cell-Type/Cell-Type Enrichment

Cell Neighborhood, Spatial Interaction Changed Features (ICF)

Cell Neighborhood, Ligand-Receptor Cell Communication

Subcellular

Segmentation

Doublet Detection

Interactive Visualizations

Interoperability

Kriging

ONTraC integration

AI technologies