Function reference • Giotto

Giotto object Create and operate on Giotto object
`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
`stitchFieldCoordinates()`	stitchFieldCoordinates
`stitchTileCoordinates()`	stitchTileCoordinates
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, …)
`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
`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
`runSpatialEnrich()`	runSpatialEnrich
`createSpatialEnrich()`	createSpatialEnrich
`runPAGEEnrich()`	runPAGEEnrich
`PAGEEnrich()`	PAGEEnrich
`runRankEnrich()`	runRankEnrich
`rankEnrich()`	rankEnrich
`runHyperGeometricEnrich()`	runHyperGeometricEnrich
`hyperGeometricEnrich()`	hyperGeometricEnrich
`runSpatialDeconv()`	runSpatialDeconv
`runDWLSDeconv()`	runDWLSDeconv
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
`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 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
2D visualization in expression space Visualization of expression space (e.g. UMAP) in 2D
`dimPlot()`	dimPlot
`plotUMAP()`	plotUMAP
`plotTSNE()`	plotTSNE
`plotPCA()`	plotPCA
`dimGenePlot()`	dimGenePlot
`dimCellPlot()`	dimCellPlot
2D visualization in spatial space Visualization in 2D spatial space
`spatPlot()`	spatPlot
`spatGenePlot()`	spatGenePlot
`spatCellPlot()`	spatCellPlot
2D visualization in spatial and expression space Visualization in both 2D spatial and expression space
`spatDimPlot()`	spatDimPlot
`spatDimGenePlot()`	spatDimGenePlot
`spatDimCellPlot()`	spatDimCellPlot
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
`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
`plotCCcomDotplot()`	plotCCcomDotplot
`plotRankSpatvsExpr()`	plotRankSpatvsExpr
`plotRecovery()`	plotRecovery
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

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 co-expression patterns / modules

HMRF

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

export from Giotto Analyzer to Viewer

Interoperability