update docs (54b62ba0) · Commits · github_fork / HdWGCNA

NAMESPACE

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		@@ -9,9 +9,11 @@ export(DimPlotMetacells)
		export(DoHubGeneHeatmap)
		export(EnrichrBarPlot)
		export(EnrichrDotPlot)
		export(GetActiveWGCNA)
		export(GetDatExpr)
		export(GetMEs)
		export(GetMultiExpr)
		export(GetWGCNAGroup)
		export(HubGeneNetworkPlot)
		export(MetacellsByGroups)
		export(ModuleConnectivity)
		@@ -22,6 +24,7 @@ export(ModuleExprScore)
		export(ModuleFeaturePlot)
		export(ModuleNetworkPlot)
		export(ModulePreservation)
		export(ModuleTFNetwork)
		export(ModuleTraitCorrelation)
		export(ModuleUMAPPlot)
		export(MotifOverlapBarPlot)
		@@ -47,8 +50,10 @@ export(RunPCAMetacells)
		export(RunUMAPMetacells)
		export(ScaleMetacells)
		export(SelectNetworkGenes)
		export(SetActiveWGCNA)
		export(SetDatExpr)
		export(SetMultiExpr)
		export(SetWGCNAGroup)
		export(SetupForWGCNA)
		export(TestSoftPowers)
		export(TestSoftPowersConsensus)

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		% Generated by roxygen2: do not edit by hand
		% Please edit documentation in R/getters_and_setters.R
		\name{GetActiveWGCNA}
		\alias{GetActiveWGCNA}
		\title{GetActiveWGCNA}
		\usage{
		GetActiveWGCNA(seurat_obj)
		}
		\arguments{
		\item{seurat_obj}{A Seurat object}
		}
		\description{
		GetActiveWGCNA
		}
		\examples{
		GetActiveWGCNA
		}
		\keyword{scRNA-seq}

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		% Generated by roxygen2: do not edit by hand
		% Please edit documentation in R/getters_and_setters.R
		\name{GetWGCNAGroup}
		\alias{GetWGCNAGroup}
		\title{GetWGCNAGroup}
		\usage{
		GetWGCNAGroup(seurat_obj, wgcna_name)
		}
		\arguments{
		\item{seurat_obj}{A Seurat object}

		\item{wgcna_name}{The name of the scWGCNA experiment in the seurat_obj@misc slot}
		}
		\description{
		GetWGCNAGroup
		}
		\examples{
		GetWGCNAGroup
		}
		\keyword{scRNA-seq}

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		% Generated by roxygen2: do not edit by hand
		% Please edit documentation in R/plotting.R
		\name{ModuleTFNetwork}
		\alias{ModuleTFNetwork}
		\title{ModuleTFNetwork}
		\usage{
		ModuleTFNetwork(
		seurat_obj,
		tf_name,
		tf_gene_name,
		edge.alpha = 0.75,
		cor_thresh = 0.25,
		high_color = "red",
		mid_color = "grey",
		low_color = "blue",
		slot = "data",
		size.scale = 30,
		tf_x = 0,
		tf_y = 0,
		wgcna_name = NULL
		)
		}
		\arguments{
		\item{seurat_obj}{A Seurat object}

		\item{tf_name}{the Motif name for the tf}

		\item{tf_gene_name}{the gene associated with this tf in the rownames(seurat_obj)}

		\item{edge.alpha}{scaling factor for edge opacity in the network}

		\item{cor_thresh}{threshold to plot correlation edges between modules}

		\item{high_color}{color for positive correlation}

		\item{mid_color}{color for zero correlation}

		\item{low_color}{color for negative correlation}

		\item{slot}{the slot in the seurat object to extract expression data for the tf_gene_name}

		\item{size.scale}{scaling factor for the size of each node}

		\item{tf_x}{x coordinate for the TF if the TF is not found in the UMAP}

		\item{tf_y}{y coordinate for the TF if the TF is not foudn in the UMAP}

		\item{wgcna_name}{the name of the WGCNA experiment in the seurat object}
		}
		\description{
		Plotting the relationships between a TF and the co-expression modules
		}
		\examples{
		ModuleTFNetwork
		}
		\keyword{scRNA-seq}

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