Function reference • hdWGCNA

Data setup Functions to set up the Seurat object for network analysis
`SetupForWGCNA()`	SetupForWGCNA
`SelectNetworkGenes()`	SelectNetworkGenes
`FindMajorIsoforms()`	FindMajorIsoforms
Metacells and metaspots Functions for constructing metacells from single-cell data and metaspots from ST data
`MetacellsByGroups()`	MetacellsByGroups
`MetaspotsByGroups()`	MetaspotsByGroups
Network Analysis Functions for constructing the co-expression network
`TestSoftPowers()`	TestSoftPowers
`TestSoftPowersConsensus()`	TestSoftPowersConsensus
`PlotSoftPowers()`	PlotSoftPowers
`ConstructNetwork()`	ConstructNetwork
`ModuleEigengenes()`	ModuleEigengenes
`ModuleConnectivity()`	ModuleConnectivity
Network Visualization Functions for visualizing the co-expression network
`ModuleNetworkPlot()`	ModuleNetworkPlot
`HubGeneNetworkPlot()`	HubGeneNetworkPlot
`RunModuleUMAP()`	RunModuleUMAP
`ModuleUMAPPlot()`	ModuleUMAPPlot
Differential analysis Functions for differential module eigengene analysis
`FindDMEs()`	FindDMEs
`FindAllDMEs()`	FindAllDMEs
`PlotDMEsVolcano()`	PlotDMEsVolcano
Enrichment Analysis Functions for Enrichr analysis and DEG overlap analysis
`RunEnrichr()`	RunEnrichr
`EnrichrBarPlot()`	EnrichrBarPlot
`EnrichrDotPlot()`	EnrichrDotPlot
`OverlapModulesDEGs()`	OverlapModulesDEGs
`OverlapBarPlot()`	OverlapBarPlot
`OverlapDotPlot()`	OverlapDotPlot
Plotting Functions for generating plots with hdWGCNA
`ModuleFeaturePlot()`	ModuleFeaturePlot
`PlotModuleTrajectory()`	PlotModuleTrajectory
Module Preservation Functions for performing module preservation analysis
`ModulePreservation()`	ModulePreservation
`PlotModulePreservation()`	PlotModulePreservation
Module Trait Correlation Functions for performing module trait correlation analysis
`ModuleTraitCorrelation()`	ModuleTraitCorrelation'
`PlotModuleTraitCorrelation()`	PlotModuleTraitCorrelation
Getters and setters Functions to retrieve and set the values for various attributes
`SetActiveWGCNA()`	SetActiveWGCNA
`GetActiveWGCNA()`	GetActiveWGCNA
`SetMetacellObject()`	SetMetacellObject
`GetMetacellObject()`	GetMetacellObject
`SetWGCNAGenes()`	SetWGCNAGenes
`GetWGCNAGenes()`	GetWGCNAGenes
`SetDatExpr()`	SetDatExpr
`GetDatExpr()`	GetDatExpr
`SetMultiExpr()`	SetMultiExpr
`GetMultiExpr()`	GetMultiExpr
`SetWGCNAParams()`	SetWGCNAParams
`GetWGCNAParams()`	GetWGCNAParams
`SetPowerTable()`	SetPowerTable
`GetPowerTable()`	GetPowerTable
`SetNetworkData()`	SetNetworkData
`GetNetworkData()`	GetNetworkData
`SetModules()`	SetModules
`GetModules()`	GetModules
`GetHubGenes()`	GetHubGenes
`SetMEs()`	SetMEs
`GetMEs()`	GetMEs
`SetMELoadings()`	SetMELoadings
`GetMELoadings()`	GetMELoadings
`SetEnrichrTable()`	SetEnrichrTable
`GetEnrichrTable()`	GetEnrichrTable
`SetModuleScores()`	SetModuleScores
`GetModuleScores()`	GetModuleScores
`GetTOM()`	GetTOM
`SetModuleUMAP()`	SetModuleUMAP
`GetModuleUMAP()`	GetModuleUMAP
`SetModuleTraitCorrelation()`	SetModuleTraitCorrelation
`GetModuleTraitCorrelation()`	GetModuleTraitCorrelation
`SetModulePreservation()`	SetModulePreservation
`GetModulePreservation()`	GetModulePreservation
`SetMotifs()`	SetMotifs
`GetMotifs()`	GetMotifs
`SetMotifMatrix()`	SetMotifMatrix
`GetMotifMatrix()`	GetMotifMatrix
`SetPFMList()`	SetPFMList
`GetPFMList()`	GetPFMList
`SetMotifTargets()`	SetMotifTargets
`GetMotifTargets()`	GetMotifTargets
`SetMotifOverlap()`	SetMotifOverlap
`GetMotifOverlap()`	GetMotifOverlap
`SetMotifScores()`	SetMotifScores
`GetMotifScores()`	GetMotifScores
Seurat wrappers Wrapper functions to run Seurat commands on the metacell data
`NormalizeMetacells()`	NormalizeMetacells
`ScaleMetacells()`	ScaleMetacells
`RunPCAMetacells()`	RunPCAMetacells
`RunHarmonyMetacells()`	RunHarmonyMetacells
`RunUMAPMetacells()`	RunUMAPMetacells
`DimPlotMetacells()`	DimPlotMetacells
Customization Customization functions
`ResetModuleColors()`	ResetModuleColors
`ResetModuleNames()`	ResetModuleNames

Reference

Data setup

Metacells and metaspots

Network Analysis

Network Visualization

Differential analysis

Enrichment Analysis

Plotting

Module Preservation

Module Trait Correlation

Getters and setters

Seurat wrappers

Customization