Function reference • Giotto

Giotto object Create and operate on Giotto object
`giotto-class` `giotto`	S4 giotto Class
`show(<giotto>)`	show method for giotto class
`createGiottoObject()`	create Giotto object
`createGiottoVisiumObject()`	createGiottoVisiumObject
`filterGiotto()`	filterGiotto
`subsetGiotto()`	subsetGiotto
`subsetGiottoLocs()`	subsetGiottoLocs
Giotto environment work with Giotto python environment
`installGiottoEnvironment()`	installGiottoEnvironment
`removeGiottoEnvironment()`	removeGiottoEnvironment
`checkGiottoEnvironment()`	checkGiottoEnvironment
import raw data functions to help to import raw spatial data
`getSpatialDataset()`	getSpatialDataset
`readExprMatrix()`	readExprMatrix
`get10Xmatrix()`	get10Xmatrix
`get10Xmatrix_h5()`	get10Xmatrix_h5
`stitchFieldCoordinates()`	stitchFieldCoordinates
`stitchTileCoordinates()`	stitchTileCoordinates
`convertEnsemblToGeneSymbol()`	convertEnsemblToGeneSymbol
add images functions to work with images for a Giotto object
`estimateImageBg()`	estimateImageBg
`changeImageBg()`	changeImageBg
`createGiottoImage()`	createGiottoImage
`addGiottoImage()`	addGiottoImage
`addGiottoImageToSpatPlot()`	addGiottoImageToSpatPlot
`showGiottoImageNames()`	showGiottoImageNames
`updateGiottoImage()`	updateGiottoImage
`getGiottoImage()`	getGiottoImage
`plotGiottoImage()`	plotGiottoImage
Giotto instructions Create or change Giotto instructions (e.g. defaults, plotting, saving, …)
`explainGiottoInstructions()`	explainGiottoInstructions
`createGiottoInstructions()`	createGiottoInstructions
`readGiottoInstructions()`	readGiottoInstrunctions
`showGiottoInstructions()`	showGiottoInstructions
`changeGiottoInstructions()`	changeGiottoInstructions
`replaceGiottoInstructions()`	replaceGiottoInstructions
Giotto helper functions Common functions to help working with Giotto objects
`pDataDT()`	pDataDT
`fDataDT()`	fDataDT
`showProcessingSteps()`	showProcessingSteps
`calculateMetaTable()`	calculateMetaTable
`calculateMetaTableCells()`	calculateMetaTableCells
`combineMetadata()`	combineMetadata
`createMetagenes()`	createMetagenes
`findNetworkNeighbors()`	findNetworkNeighbors
Giotto processing functions Functions that will (help to) add, update or change the Giotto object when processing spatial data
`filterDistributions()`	filterDistributions
`filterCombinations()`	filterCombinations
`normalizeGiotto()`	normalizeGiotto
`adjustGiottoMatrix()`	adjustGiottoMatrix
`annotateGiotto()`	annotateGiotto
`removeCellAnnotation()`	removeCellAnnotation
`removeGeneAnnotation()`	removeGeneAnnotation
`addCellMetadata()`	addCellMetadata
`addGeneMetadata()`	addGeneMetadata
`addGeneStatistics()`	addGeneStatistics
`addCellStatistics()`	addCellStatistics
`addStatistics()`	addStatistics
`addGenesPerc()`	addGenesPerc
`addCellIntMetadata()`	addCellIntMetadata
dimension reduction Functions to reduce dimensions
`calculateHVG()`	calculateHVG
`signPCA()`	signPCA
`screePlot()`	screePlot
`jackstrawPlot()`	jackstrawPlot
`runPCA()`	runPCA
`runUMAP()`	runUMAP
`runtSNE()`	runtSNE
Clustering Functions to cluster cells
`createNearestNetwork()`	createNearestNetwork
`addNetworkLayout()`	addNetworkLayout
`extractNearestNetwork()`	extractNearestNetwork
`clusterCells()`	clusterCells
`doLeidenCluster()`	doLeidenCluster
`doLouvainCluster()`	doLouvainCluster
`doKmeans()`	doKmeans
`doHclust()`	doHclust
`doSNNCluster()`	doSNNCluster
`doRandomWalkCluster()`	doRandomWalkCluster
`subClusterCells()`	subClusterCells
`doLeidenSubCluster()`	doLeidenSubCluster
`doLouvainSubCluster()`	doLouvainSubCluster
`getClusterSimilarity()`	getClusterSimilarity
`mergeClusters()`	mergeClusters
`getDendrogramSplits()`	getDendrogramSplits
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 Different visualization options to explore gene, cell or cluster characteristics
`showClusterHeatmap()`	showClusterHeatmap
`showClusterDendrogram()`	showClusterDendrogram
`plotHeatmap()`	plotHeatmap
`plotMetaDataHeatmap()`	plotMetaDataHeatmap
`plotMetaDataCellsHeatmap()`	plotMetaDataCellsHeatmap
`violinPlot()`	violinPlot
Spatial enrichment & deconvolution algorithms to compute spatial enrichment of gene signatures or single-cell RNAseq annotation
`makeSignMatrixPAGE()`	makeSignMatrixPAGE
`makeSignMatrixRank()`	makeSignMatrixRank
`makeSignMatrixDWLS()`	makeSignMatrixDWLS
`makeSignMatrixDWLSfromMatrix()`	makeSignMatrixDWLSfromMatrix
`runSpatialEnrich()`	runSpatialEnrich
`createSpatialEnrich()`	createSpatialEnrich
`runPAGEEnrich()`	runPAGEEnrich
`PAGEEnrich()`	PAGEEnrich
`runRankEnrich()`	runRankEnrich
`rankEnrich()`	rankEnrich
`runHyperGeometricEnrich()`	runHyperGeometricEnrich
`hyperGeometricEnrich()`	hyperGeometricEnrich
`runSpatialDeconv()`	runSpatialDeconv
`runDWLSDeconv()`	runDWLSDeconv
`spatDeconvPlot()`	spatDeconvPlot
Spatial network or grid Function to (help) create a spatial network or grid
`spatNetwDistributionsDistance()`	spatNetwDistributionsDistance
`spatNetwDistributionsKneighbors()`	spatNetwDistributionsKneighbors
`spatNetwDistributions()`	spatNetwDistributionsDistance
`createSpatialDelaunayNetwork()`	createSpatialDelaunayNetwork
`plotStatDelaunayNetwork()`	plotStatDelaunayNetwork
`createSpatialKNNnetwork()`	createSpatialKNNnetwork
`createSpatialNetwork()`	createSpatialNetwork
`annotateSpatialNetwork()`	annotateSpatialNetwork
`annotateSpatialGrid()`	annotateSpatialGrid
`createSpatialDefaultGrid()`	createSpatialDefaultGrid
`createSpatialGrid()`	createSpatialGrid
`showNetworks()`	showNetworks
`showGrids()`	showGrids
Spatial genes Functions to identify spatial genes
`binSpect()`	binSpect
`binSpectSingle()`	binSpectSingle
`binSpectMulti()`	binSpectMulti
`silhouetteRank()`	silhouetteRank
`spatialDE()`	spatialDE
`spatialAEH()`	spatialAEH
`trendSceek()`	trendSceek
`spark()`	spark
Spatial gene simulation Functions to simulate a gene expression pattern
`simulateOneGenePatternGiottoObject()`	simulateOneGenePatternGiottoObject
`runPatternSimulation()`	runPatternSimulation
Spatial co-expression patterns / modules Functions to identify spatial co-expression patterns
`clusterSpatialCorGenes()`	clusterSpatialCorGenes
`detectSpatialCorGenes()`	detectSpatialCorGenes
`heatmSpatialCorGenes()`	heatmSpatialCorGenes
`showSpatialCorGenes()`	showSpatialCorGenes
`rankSpatialCorGroups()`	rankSpatialCorGroups
HMRF Functions to identify spatial domains with HMRF
`doHMRF()`	doHMRF
`loadHMRF()`	loadHMRF
`viewHMRFresults()`	viewHMRFresults
`writeHMRFresults()`	writeHMRFresults
`addHMRF()`	addHMRF
`viewHMRFresults2D()`	viewHMRFresults2D
`viewHMRFresults3D()`	viewHMRFresults3D
HMRF V2 Functions to identify spatial domains with HMRF V2 (test)
`chooseAvailableSpatialGenes()`	chooseAvailableSpatialGenes
`checkAndFixSpatialGenes()`	checkAndFixSpatialGenes
`filterSpatialGenes()`	filterSpatialGenes
`initHMRF_V2()`	initHMRF_V2
`doHMRF_V2()`	doHMRF_V2
`addHMRF_V2()`	addHMRF_V2
`viewHMRFresults_V2()`	viewHMRFresults_V2
2D visualization in expression space Visualization of expression space (e.g. UMAP) in 2D
`dimPlot()`	dimPlot
`dimPlot2D()`	dimPlot2D
`plotUMAP()`	plotUMAP
`plotUMAP_2D()`	plotUMAP_2D
`plotTSNE()`	plotTSNE
`plotTSNE_2D()`	plotTSNE_2D
`plotPCA()`	plotPCA
`plotPCA_2D()`	plotPCA_2D
`dimGenePlot()`	dimGenePlot
`dimGenePlot2D()`	dimGenePlot2D
`dimCellPlot()`	dimCellPlot
`dimCellPlot2D()`	dimCellPlot2D
2D visualization in spatial space Visualization in 2D spatial space
`spatPlot()`	spatPlot
`spatPlot2D()`	spatPlot2D
`spatGenePlot()`	spatGenePlot
`spatGenePlot2D()`	spatGenePlot2D
`spatCellPlot()`	spatCellPlot
`spatCellPlot2D()`	spatCellPlot2D
2D visualization in spatial and expression space Visualization in both 2D spatial and expression space
`spatDimPlot()`	spatDimPlot
`spatDimPlot2D()`	spatDimPlot2D
`spatDimGenePlot()`	spatDimGenePlot
`spatDimGenePlot2D()`	spatDimGenePlot2D
`spatDimCellPlot()`	spatDimCellPlot
`spatDimCellPlot2D()`	spatDimCellPlot2D
3D dimension reduction visualization Visualization of expression space (e.g. UMAP) in 3D
`dimPlot3D()`	dimPlot3D
`plotUMAP_3D()`	plotUMAP_3D
`plotTSNE_3D()`	plotTSNE_3D
`plotPCA_3D()`	plotPCA_3D
`dimGenePlot3D()`	dimGenePlot3D
3D visualization in spatial space Visualization in 3D spatial space
`spatPlot3D()`	spatPlot3D
`spatGenePlot3D()`	spatGenePlot3D
3D visualization in spatial and expression space Visualization in both 3D spatial and expression space
`spatDimPlot3D()`	spatDimPlot3D
`spatDimGenePlot3D()`	spatDimGenePlot3D
In silico cross sections create in silico 2D cross sections from 3D data
`createCrossSection()`	createCrossSection
`crossSectionGenePlot()`	crossSectionGenePlot
`crossSectionPlot()`	crossSectionPlot
`crossSectionGenePlot3D()`	crossSectionGenePlot3D
`crossSectionPlot3D()`	crossSectionPlot3D
`insertCrossSectionSpatPlot3D()`	insertCrossSectionSpatPlot3D
`insertCrossSectionGenePlot3D()`	insertCrossSectionGenePlot3D
cell neighborhood; cell-type/cell-type enrichment calculate and visualize cell-type/cell-type spatial enrichment or depletion
`cellProximityEnrichment()`	cellProximityEnrichment
`cellProximityBarplot()`	cellProximityBarplot
`cellProximityHeatmap()`	cellProximityHeatmap
`cellProximityNetwork()`	cellProximityNetwork
`cellProximitySpatPlot()`	cellProximitySpatPlot
`cellProximitySpatPlot2D()`	cellProximitySpatPlot2D
`cellProximitySpatPlot3D()`	cellProximitySpatPlot2D
cell neighborhood; spatial interaction changed genes Identify and visualize genes that change in a source cell type due to interaction with another neighboring cell type
`findInteractionChangedGenes()`	findInteractionChangedGenes
`findICG()`	findICG
`findCellProximityGenes()`	findCellProximityGenes
`findCPG()`	findCPG
`filterCellProximityGenes()`	filterCellProximityGenes
`filterInteractionChangedGenes()`	filterInteractionChangedGenes
`filterICG()`	filterICG
`filterCPG()`	filterCPG
`combineInteractionChangedGenes()`	combineInteractionChangedGenes
`combineICG()`	combineICG
`combineCellProximityGenes()`	combineCellProximityGenes
`combineCPG()`	combineCPG
`plotInteractionChangedGenes()`	plotInteractionChangedGenes
`plotICG()`	plotICG
`plotCellProximityGenes()`	plotCellProximityGenes
`plotCPG()`	plotCPG
`plotCombineInteractionChangedGenes()`	plotCombineInteractionChangedGenes
`plotCombineICG()`	plotCombineICG
`plotCombineCellProximityGenes()`	plotCombineCellProximityGenes
`plotCombineCPG()`	plotCombineCPG
cell neighborhood; ligand-receptor cell communication Find putative increased spatial ligand-receptor activity between cells of pairs of cell types
`exprCellCellcom()`	exprCellCellcom
`spatCellCellcom()`	spatCellCellcom
`combCCcom()`	combCCcom
`plotCCcomDotplot()`	plotCCcomDotplot
`plotCCcomHeatmap()`	plotCCcomHeatmap
`plotCombineCellCellCommunication()`	plotCombineCellCellCommunication
`plotCombineCCcom()`	plotCombineCCcom
`plotRankSpatvsExpr()`	plotRankSpatvsExpr
`plotRecovery()`	plotRecovery
`specificCellCellcommunicationScores()`	specificCellCellcommunicationScores
cell neighborhood; within a multi-cell spot NA
`cellProximityEnrichmentSpots()`	cellProximityEnrichmentSpots
`geneExpDWLS()`	geneExpDWLS
`cellProximityEnrichmentEachSpot()`	cellProximityEnrichmentEachSpot
`findICGSpot()`	findICGSpot
`filterICGSpot()`	filterICGSpot
`plotICGSpot()`	plotICGSpot
`plotCellProximityGenesSpot()`	plotCellProximityGenesSpot
`spatCellCellcomSpots()`	spatCellCellcomSpots
export from Giotto Analyzer to Viewer Export selected annotations to a folder that can be used as input for Giotto Viewer
`exportGiottoViewer()`	exportGiottoViewer
Interoperability Convert other type of objects into a Giotto object
`anndataToGiotto()`	anndataToGiotto
Auxiliary functions Functions to facilitate spatial data analysis and visualization
`getDistinctColors()`	getDistinctColors
`showSaveParameters()`	showSaveParameters
`processGiotto()`	processGiotto
`createRegZStackGobject()`	createRegZStackGobject
`create_crossSection_object()`	create_crossSection_object
`plotRecovery_sub()`	plotRecovery_sub
Mini datasets Ready to use mini datasets
`mini_giotto_multi_cell`	mini Giotto object for spatial multi-cell resolution data
`mini_giotto_single_cell`	mini Giotto object for spatial single-cell resolution data
`mini_giotto_3D`	mini Giotto object for spatial single-cell 3D data

Reference

Giotto object

Giotto environment

import raw data

add images

Giotto instructions

Giotto helper functions

Giotto processing functions

dimension reduction

Clustering

Marker genes

Auxiliary visualizations

Spatial enrichment & deconvolution

Spatial network or grid

Spatial genes

Spatial gene simulation

Spatial co-expression patterns / modules

HMRF

HMRF V2

2D visualization in expression space

2D visualization in spatial space

2D visualization in spatial and expression space

3D dimension reduction visualization

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 genes

cell neighborhood; ligand-receptor cell communication

cell neighborhood; within a multi-cell spot

export from Giotto Analyzer to Viewer

Interoperability

Auxiliary functions

Mini datasets