Function Documentation

Giotto Handing Functions

Giotto Instructions

Create or change Giotto instructions (e.g. defaults, plotting, saving, etc.)

Function	Description
createGiottoInstructions()	Create Giotto Instructions
readGiottoInstructions()	Read Giotto Instructions
showGiottoInstructions()	Show Giotto Instructions
changeGiottoInstructions()	Change Giotto Instructions
replaceGiottoInstructions()	Replace Giotto Instructions

Giotto Object

Create and operate on Giotto Object

Function	Description
createGiottoObject()	Create a Giotto object
createGiottoVisiumObject()	Create a Visium Object
filterGiotto()	Filter Giotto
subsetGiotto()	Subset Giotto
subsetGiottoLocs()	Subset Giotto Locs

Giotto Environment

Work with Giotto Python Environment

Function	Description
installGiottoEnvironment()	Install Giotto Environment
removeGiottoEnvironment()	Remove Giotto Environment
checkGiottoEnvironment()	Check Giotto Environment

Giotto Helper Functions

Common functions to help working with Giotto objects

Function	Description
pDataDT()	Show Cell Metadata
fDataDT()	Show Gene Metadata
showProcessingSteps()	Show Sequential Processing Steps
calculateMetaTable()	Calculate Average Gene Expression
calculateMetaTableCells()	Calculate the Average Metadata Values
combineMetadata()	Combine Cell Metadata
createMetagenes()	Create Average Metagene
findNetworkNeighbors()	Find Spatial Neighbors

Giotto Processing Functions

Functions that will (help to) add, update or change the Giotto object when processing spatial data.

Function	Description
filterDistributions()	Show Gene Distributions
filterCombinations()	Show Gene/Cell Loss
normalizeGiotto()	Normalize And/Or Scale Expression Values
adjustGiottoMatrix()	Adjust Expression Values
annotateGiotto()	Convert Cluster Results Into User Provided Annotation
removeCellAnnotation()	Remove Cell Annotation
removeGeneAnnotation()	Remove Gene Annotation
addCellMetadata()	Add Cell Metadata
addGeneMetadata()	Add Gene Metadatat
addGeneStatistics()	Add Gene Statistics
addCellStatistics()	Add Cell Statistics
addStatistics()	Add Gene and Cell Statistics
addGenesPerc()	Calculate Percent Counts
addCellIntMetadata()	Add Cell Metadata Information Column

Import Raw Data

Functions to help to import raw spatial data.

Function	Description
getSpatialDataset()	Get The Spatial Data
readExprMatrix()	Read The Expression Matrix
get10Xmatrix()	Get An Expression Matrix From 10X Structure
get10Xmatrix_h5()	Get An Expression Matrix From 10X h5 Path
stitchFieldCoordinates()	Stitch Field Coordinates Together
stitchTileCoordinates()	Stitch Tile Coordinates Together

Adding Images

Functions to work with images for a Giotto object.

Function	Description
estimateImageBg()	Estimate Background Color
changeImageBg()	Change Background Color
createGiottoImage()	Create a Giotto Image
addGiottoImage()	Add a Giotto Image to Giotto Object
addGiottoImageToSpatPlot()	Add Giotto Image to Spatial ggplot
showGiottoImageNames()	Print Attached Giotto Image
updateGiottoImage()	Update Giotto Image Boundaries
getGiottoImage()	Get Giotto Image From Giotto Object
plotGiottoImage()	Plot A Giotto Image From A Giotto Object

Dimension Reduction

Functions to reduce dimensions.

Function	Description
calculateHVG()	Compute Highly Variable Genes
signPCA()	Identify PC’s
screePlot()	Identify Significant PCs Via Screeplot
jackstrawPlot()	Identify Significant PCs Via JackstrawPlot
runPCA()	Run A PCA
runUMAP()	Run A UMAP
runtSNE()	Run a tSNE

Clustering

Functions to cluster cells.

Function	Description
createNearestNetwork()	Create NN Network
addNetworkLayout()	Add Network Layout
extractNearestNetwork()	Calculate Gene Signature Enrichment Score
clusterCells()	Cluster Cells
doLeidenCluster()	Cluster Cells Using NN-Network
doLouvainCluster()	Cluster Cells Using NN-Network and Louvain Algorithm
doKmeans()	Cluster Cells Using K-Means
doHclust()	Cluster Cells Using Hierarchical Clustering
subClusterCells()	Sub-Cluster Cells
doLeidenSubCluster()	Further Sub-Clustering of Cells Using NN-Network and Leiden Algorithm
doLouvainSubCluster()	Further Sub-Clustering of Cells Using NN-Network and Louvain Algorithm
getClusterSimilarity()	Determine Pairwise Correlation Score
mergeClusters()	Merge Clusters
getDendrogramSplits()	Split Dendrogram

Marker Genes

Functions to detect cell type / cluster specific marker genes.

Function	Description
findMarkers()	Find Marker Genes
findMarkers_one_vs_all()	Find Marker Genes At Once
findGiniMarkers()	Find Gini Markers
findGiniMarkers_one_vs_all()	Find Marker Genes Using Gini in One vs. All Manner
findScranMarkers()	Identify Marker Genes Based on Scran
findScranMarkers_one_vs_all()	Identify Marker Genes in a One vs. All Manner
findMastMarkers()	Identify Marker Genes Using MAST
findMastMarkers_one_vs_all()	Identify Marker Genes Using MAST in One vs. All Manner

Auxiliary Visualizations

Functions for different visualization options to explore gene, cell or cluster characteristics.

Function	Description
showClusterHeatmap()	Create Cluster Heatmap
showClusterDendrogram()	Create Cluster Dendrogram
plotHeatmap()	Plot Heatmap
plotMetaDataHeatmap()	Plot Heatmap for Metadata
plotMetaDataCellsHeatmap()	Plot Heatmap for Cell Metdata
violinPlot()	Create Violin Plot

Spatial

Enrichment & Deconvolution

Functions for algorithms to compute spatial enrichment of gene signatures or single-cell RNA-seq annotation.

Function	Description
makeSignMatrixPAGE()	Convert Gene Signature List To Binary Matrix
makeSignMatrixRank()	Convert Single-Cell Matrix to Cluster
runSpatialEnrich()	Calculate Gene Signature Enrichment Score With RANK
createSpatialEnrich()	Calculate Gene Signature Enrichment Scores
runPAGEEnrich()	Calculate Position Gene Signature Enrichment With PAGE
PAGEEnrich()	Calculate Gene Signature Enrichment With PAGE
runRankEnrich()	Calculate Gene Signature Enrichment Using RANK
rankEnrich()	Calculate Gene Signature Enrichment Score With RANK
runHyperGeometricEnrich()	Calculate Gene Signature Enrichment Score With Hypergeometric Test
hyperGeometricEnrich()	Calculate Gene Signature Enrichment Score With Hypergeometric Test
runSpatialDeconv()	Perform Deconvolution
runDWLSDeconv()	Perform DWLS Deconvolution

Spatial Network Or Grid

Function to (help) create a spatial network or grid.

Function	Description
spatNetwDistributionsDistance()	Distance Distribution for Spatial k-Neighbor
spatNetwDistributionsKneighbors()	Distance Distribution for Spatial k-Neighbor
spatNetwDistributions()	Histogram of Distance Distribution for Spatial k-Neighbors
createSpatialDelaunayNetwork()	Create Spatial Delaunay
plotStatDelaunayNetwork()	Plot Network Statistics for Delaunay Network
createSpatialKNNnetwork()	Create Spatial KNN Network
createSpatialNetwork()	Create Spatial Network
annotateSpatialNetwork()	Annotate Spatial Network
annotateSpatialGrid()	Annotate Spatial Grid
createSpatialGrid()	Create Spatial Grid
showNetworks()	Print Available Spatial Networks
showGrids()	Print Available Spatial Grids

Spatial Genes

Functions to identify spatial genes.

Function	Description
binSpect()	Create BinSpect
binSpectSingle()	Create binSpect For Single Network
binSpectMulti()	binSpect for Multiple KNN Networks
silhouetteRank()	Create binSpect For Single Network
spatialDE()	Compute Spatial Variables With SpatialDE Method
spatialAEH()	Compute Spatial Variables With SpatialAEH Method
trendSceek()	Compute Spatially Variable Genes With Trendsceek
spark()	Compute Spatially Variable Genes With SPARK

Spatial Gene Simulation

Functions to simulate a gene expression pattern.

Function	Description
simulateOneGenePatternGiottoObject()	Create Simulated Spatial Pattern
runPatternSimulation()	Create Known Spatial Pattern for Selected Genes

Spatial Co-Expression Patterns/Modules

Functions to identify spatial co-expression patterns.

Function	Description
clusterSpatialCorGenes()	Cluster Genes Using Spatial Information
detectSpatialCorGenes()	Detect Genes Using Spatial Correlation
heatmSpatialCorGenes()	Create Heatmap of Spatial Correlation
showSpatialCorGenes()	Show Spatially Correlated Genes
rankSpatialCorGroups()	Rank Spatially Correlated Gene Clusters

Hidden Markov Random Field (HMRF)

Functions to identify spatial domains with HMRF.

Function	Description
doHMRF()	Rank Spatially Correlated Gene Clusters
loadHMRF()	Load HMRF
viewHMRFresults()	View HMRF Results
writeHMRFresults()	Write doHMRF() Results
addHMRF()	Add doHMRF() Results
viewHMRFresults2D()	View HMRF Results
viewHMRFresults3D()	View HMRF Results

2D Visualization

In Expression Space

Visualization of expression space (e.g. UMAP) in 2D.

Function	Description
dimPlot()	Visualize Cells By Coordinates
plotUMAP()	UMAP Wrapper
plotTSNE()	tSNE Wrapper
plotPCA()	PCA Wrapper
dimGenePlot()	Visualize Gene Expression By Dimension Coordinates
dimCellPlot()	Visualize Cells Expression By Dimension Coordinates

In Spatial Space

Visualization of expression space (e.g. UMAP) in 2D.

Function	Description
spatPlot()	Visualize Cells By Spatial Coordinates
spatGenePlot()	Visualize Cells and Genes By Spatial Coordinates
spatCellPlot()	Visualize Cells By Spatial Coordinates

In Both Spatial And Expression Space

Visualization in both 2D spatial and expression space.

Function	Description
spatDimPlot()	Visualize Cells By Spatial and Dimensional Coordinates
spatDimGenePlot()	Visualize Genes By Spatial and Dimension Coordinates Via ggplot
spatDimCellPlot()	Visualize Cells By Spatial And Dimension Coordinates in 2D

3D Visualization

Dimension Reduction

Visualization in both 2D spatial and expression space.

Function	Description
dimPlot2D()	Visualize Cells By Spatial Coordinates in 2D
dimPlot3D()	Visualize Cells By Spatial Coordinates in 3D
plotUMAP_3D()	Visualize Cells By Spatial Coordinates in 3D
plotTSNE_3D()	Visualize Cells By Dimension Reduction Coordinates in 3D
plotPCA_3D()	Visualize Cells By 3D PCA Dimension Reduction
dimGenePlot3D()	Visualize Cells And Gene Expression By Dimension Reduction

In Spatial Space

Visualization in both 2D spatial and expression space.

Function	Description
spatPlot3D()	Visualize Cells By Spatial and Dimensional Coordinates in 3D
spatDimGenePlot3D()	Visualize Cells By Spatial and Dimensional Coordinates Using Plotly

In Silico Cross Sections

Functions to create an in silico 2D cross sections from 3D data.

Function	Description
createCrossSection()	Create a Virtual Cross Section
crossSectionGenePlot()	Visualize Cells And Gene Expression Virtually
crossSectionPlot()	Visualize Cells In Virtual Cross Section
crossSectionGenePlot3D()	Visualize Cells And Gene Expression Virtually (3D)
crossSectionPlot3D()	Visualize Cells In A Virtual Cross Section (3D)
insertCrossSectionSpatPlot3D()	Visualize Mesh-Grid Lines With Cells
insertCrossSectionGenePlot3D()	Visualize Cells And Gene Expression In A Virtual Cross Section

Cell Neighborhood

Cell-Type/Cell-Type Enrichment

Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.

Function	Description
cellProximityEnrichment()	Calculate Cell-Cell Interaction Enrichment
cellProximityBarplot()	Create Barplot from Cell-Cell Proximity Score
cellProximityHeatmap()	Create Heatmap from Cell-Cell Proximity Score
cellProximityNetwork()	Create Network from Cell-Cell Proximity Score
cellProximitySpatPlot()	Visualize Cell-Cell Interactions (2D)
cellProximitySpatPlot3D()	Visualize Cell-Cell Interactions (3D)

Spatial Interaction Changed Genes (ICG)

Identify and visualize genes that change in a source cell type due to interaction with another neighboring cell type.

Function	Description
findInteractionChangedGenes()	Identify Cell-Cell Interaction Changed Genes (ICGs)
findICG()	Identify Cell-Cell Interaction Changed Genes (ICGs)
findCellProximityGenes()	Identify Cell-Cell Interaction Changed Genes (ICGs)
findCPG()	Identify Cell-Cell Interaction Changed Genes (ICGs)
filterCellProximityGenes()	Identify Cell-Cell Interaction Changed Genes (ICGs)
filterInteractionChangedGenes()	Filter The Identified Cell-Cell Interaction Changed Genes (ICGs)
filterICG()	Filter ICGs
filterCPG()	Filter ICGs
combineInteractionChangedGenes()	Combine ICG Scores (Pairwise)
combineICG()	Combine ICG Scores (Pairwise)
combineCellProximityGenes()	Combine ICG Scores (Pairwise)
combineCPG()	Combine ICG Scores (Pairwise)
plotInteractionChangedGenes()	Visualize ICGs via Barplot
plotICG()	Visualize ICGs via Barplot
plotCellProximityGenes()	Visualize Cell Proximity Gene Scores
plotCPG()	Visualize Cell Proximity Gene Scores
plotCombineInteractionChangedGenes()	Visualize Combined ICG Scores
plotCombineICG()	Visualize Combined ICG Scores
plotCombineCellProximityGenes()	Visualize Combined ICG Scores
plotCombineCPG()	Visualize Combined ICG Scores

Ligand-Receptor Cell Communication

Functions to calculate and visualize cell-type/cell-type spatial enrichment or depletion.

Function	Description
exprCellCellcom()	Calculate Cell-Cell Communication Scores
spatCellCellcom()	Calculate Spatial Cell-Cell Communication Scores
plotCCcomDotplot()	Plot Ligand-Receptor Communication Scores
plotRankSpatvsExpr()	Plot Comparison of Ligand-Receptor Rankings
plotRecovery()	Plot Comparison of Ligand-Receptor Rankings

Export From Giotto Analyzer To Viewer

Export selected annotations to a folder that can be used as input for Giotto Viewer.

Function	Description
exportGiottoViewer()	Compute Highly Variable Genes

Interoperability

Convert other type of objects into a Giotto object.

Function	Description
anndataToGiotto()	Compute Highly Variable Genes