update docs (2b908e35) · Commits · github_fork / HdWGCNA

NAMESPACE

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		@@ -10,10 +10,30 @@ export(DoHubGeneHeatmap)
		export(EnrichrBarPlot)
		export(EnrichrDotPlot)
		export(GetActiveWGCNA)
		export(GetAvgModuleExpr)
		export(GetDatExpr)
		export(GetEnrichrTable)
		export(GetMEs)
		export(GetMetacellObject)
		export(GetModulePreservation)
		export(GetModuleScores)
		export(GetModuleTraitCorrelation)
		export(GetModuleUMAP)
		export(GetModules)
		export(GetMotifMatrix)
		export(GetMotifOverlap)
		export(GetMotifScores)
		export(GetMotifTargets)
		export(GetMotifs)
		export(GetMultiExpr)
		export(GetNetworkData)
		export(GetPFMList)
		export(GetPowerTable)
		export(GetROCData)
		export(GetTOM)
		export(GetWGCNAGenes)
		export(GetWGCNAGroup)
		export(GetWGCNAParams)
		export(HubGeneNetworkPlot)
		export(MetacellsByGroups)
		export(ModuleConnectivity)
		@@ -51,12 +71,35 @@ export(RunUMAPMetacells)
		export(ScaleMetacells)
		export(SelectNetworkGenes)
		export(SetActiveWGCNA)
		export(SetAvgModuleExpr)
		export(SetDatExpr)
		export(SetEnrichrTable)
		export(SetMEs)
		export(SetMetacellObject)
		export(SetModulePreservation)
		export(SetModuleScores)
		export(SetModuleTraitCorrelation)
		export(SetModuleUMAP)
		export(SetModules)
		export(SetMotifMatrix)
		export(SetMotifOverlap)
		export(SetMotifScores)
		export(SetMotifTargets)
		export(SetMotifs)
		export(SetMultiExpr)
		export(SetNetworkData)
		export(SetPFMList)
		export(SetPowerTable)
		export(SetROCData)
		export(SetWGCNAGenes)
		export(SetWGCNAGroup)
		export(SetWGCNAParams)
		export(SetupForWGCNA)
		export(TestSoftPowers)
		export(TestSoftPowersConsensus)
		export(TransferModuleGenome)
		export(construct_metacells)
		export(metacells_by_groups)
		export(scale01)
		export(shuffle_points)
		export(umap_theme)

R/getters_and_setters.R

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R/helpers.R

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		# scale between 0 & 1


		#' scale01
		#'
		#' Function to scale a numeric vector between 0 and 1.
		#'
		#' @param x numeric vector
		#' @keywords scRNA-seq
		#' @export
		#' @examples scale01
		scale01 <- function(x){
		y <- min(x); z <- max(x);
		(x-y) / (z-y)
		}



		#' umap_theme
		#'
		#' ggplot theme to remove axes etc.
		#'
		#' @keywords scRNA-seq
		#' @export
		#' @examples umap_theme
		umap_theme <- function(){
		theme(
		axis.line=element_blank(),
		@@ -21,7 +39,16 @@ umap_theme <- function(){
		)
		}

		# helper function to shuffle points when plotting:


		#' shuffle_points
		#'
		#' Function to shuffle the rows of a dataframe.
		#'
		#' @param df dataframe
		#' @keywords scRNA-seq
		#' @export
		#' @examples shuffle_points
		shuffle_points <- function(df){
		return(df[sample(1:dim(df)[1], dim(df)[1]),])
		}

docs/articles/basic_tutorial.html

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docs/articles/customization.html

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		@@ -181,7 +181,7 @@
		<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">MetBrewer</span><span class="op">)</span>

		<span class="co"># get a table of just the module and it's unique color</span>
		<span class="va">mod_color_df</span> <span class="op"><-</span> <span class="fu">GetModules</span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
		<span class="va">mod_color_df</span> <span class="op"><-</span> <span class="fu"><a href="../reference/GetModules.html">GetModules</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
		<span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">module</span>, <span class="va">color</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
		<span class="va">distinct</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">module</span><span class="op">)</span>

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