Giotto Environment

Install and work with Giotto Python Environment.

installGiottoEnvironment()

installGiottoEnvironment (from GiottoClass)

removeGiottoEnvironment()

removeGiottoEnvironment (from GiottoClass)

checkGiottoEnvironment()

checkGiottoEnvironment (from GiottoClass)

Giotto Instructions

Create or change Giotto instructions.

createGiottoInstructions()

Create instructions for giotto functions (from GiottoClass)

readGiottoInstructions()

Read giotto instructions associated with giotto object (from GiottoClass)

changeGiottoInstructions()

Change giotto instruction(s) associated with giotto object (from GiottoClass)

replaceGiottoInstructions()

Replace all giotto instructions in giotto object (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

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

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

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()

Show giotto instructions associated with giotto object (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 clustering (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)

addFeatStatistics()

Add feature statistics

addCellStatistics()

addCellStatistics

addStatistics()

addStatistics

addFeatsPerc()

addFeatsPerc

addCellIntMetadata()

addCellIntMetadata

processGiotto()

processGiotto

filterCPG()

filterCPG

Dimension Reduction

Functions to reduce dimensions.

calculateHVF()

calculateHVF

signPCA()

signPCA

screePlot()

screePlot

create_screeplot()

create_screeplot

jackstrawPlot()

jackstrawPlot

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()

subClusterCells

doLeidenSubCluster()

doLeidenSubCluster

doLouvainSubCluster()

doLouvainSubCluster

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()

makeSignMatrixPAGE

makeSignMatrixRank()

makeSignMatrixRank

runSpatialEnrich()

runSpatialEnrich

runPAGEEnrich()

runPAGEEnrich

runPAGEEnrich_OLD()

runPAGEEnrich_OLD

runRankEnrich()

runRankEnrich

rankEnrich()

rankEnrich

runHyperGeometricEnrich()

runHyperGeometricEnrich

hyperGeometricEnrich()

hyperGeometricEnrich

PAGEEnrich()

PAGEEnrich

createSpatialEnrich()

createSpatialEnrich

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)

Spatial Expression Patterns

Methods to detect spatially coherent expression patterns.

binSpectSingleMatrix()

binSpectSingleMatrix

binSpectSingle()

binSpectSingle

binSpectMultiMatrix()

binSpectMultiMatrix

binSpectMulti()

binSpectMulti

binSpect()

binSpect

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()

detectSpatialCorFeats

detectSpatialCorGenes()

detectSpatialCorGenes

clusterSpatialCorGenes()

clusterSpatialCorGenes

detectSpatialCorFeatsMatrix()

detectSpatialCorFeatsMatrix

detectSpatialPatterns()

detectSpatialPatterns

heatmSpatialCorFeats()

heatmSpatialCorFeats

heatmSpatialCorGenes()

heatmSpatialCorGenes

showSpatialCorFeats()

showSpatialCorFeats

showSpatialCorGenes()

showSpatialCorGenes

rankSpatialCorGroups()

rankSpatialCorGroups

getBalancedSpatCoexpressionFeats()

getBalancedSpatCoexpressionFeats

Spatial Data Handling

Functions to condense spatial data.

combineSpatialCellFeatureInfo()

combineSpatialCellFeatureInfo (from GiottoClass)

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

crossSectionGenePlot()

crossSectionGenePlot

crossSectionPlot()

crossSectionPlot

crossSectionGenePlot3D()

crossSectionGenePlot3D

crossSectionPlot3D()

crossSectionPlot3D

insertCrossSectionGenePlot3D()

insertCrossSectionGenePlot3D

insertCrossSectionSpatPlot3D()

insertCrossSectionSpatPlot3D

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

specificCellCellcommunicationScores()

specificCellCellcommunicationScores

filterCellProximityGenes()

filterCellProximityGenes

findCellProximityGenes()

findCellProximityGenes

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()

findInteractionChangedFeats

findICF()

findICF

findICFSpot()

findICFSpot

findICG()

findICG

findCPG()

findCPG

filterInteractionChangedFeats()

filterInteractionChangedFeats

filterInteractionChangedGenes()

filterInteractionChangedGenes

filterICF()

filterICF

filterICFSpot()

filterICFSpot

filterICG()

filterICG

plotICF()

Plot interaction changed features

plotICFSpot()

plotICFSpot

plotCellProximityFeats()

plotCellProximityFeats

plotCPF()

plotCPF

combineInteractionChangedFeats()

combineInteractionChangedFeats

combineICF()

combineICF

plotCombineInteractionChangedFeats()

plotCombineInteractionChangedFeats

plotInteractionChangedFeats()

Plot interaction changed features

plotCombineICF()

plotCombineICF

combineCPG()

combineCPG

combineCellProximityGenes()

combineCellProximityGenes

combineICG()

combineICG

combineInteractionChangedGenes()

combineInteractionChangedGenes

findInteractionChangedGenes()

findInteractionChangedGenes

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()

combCCcom

exprCellCellcom()

exprCellCellcom

spatCellCellcom()

spatCellCellcom

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)

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

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

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)

anndataToGiotto()

Convert anndata to Giotto (from GiottoClass)

giottoMasterToSuite()

Convert a master Giotto object to suite (from GiottoClass)

convertEnsemblToGeneSymbol()

convertEnsemblToGeneSymbol