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