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

get10Xmatrix_h5()

get10Xmatrix_h5

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 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

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