module customization tutorial (bc726104) · Commits · github_fork / HdWGCNA

NAMESPACE

+2 −0

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		@@ -34,6 +34,8 @@ export(OverlapModulesMotifs)
		export(PlotDendrogram)
		export(ProjectModules)
		export(ROCCurves)
		export(ResetModuleColors)
		export(ResetModuleNames)
		export(RunEnrichr)
		export(RunHarmonyMetacells)
		export(RunModuleUMAP)

R/WGCNA_functions.R

+3 −4

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		@@ -1619,9 +1619,8 @@ MotifTargetScore <- function(
		#' Run UMAP on co-expression matrix using hub genes as features.
		#'
		#' @param seurat_obj A Seurat object
		#' @param n_hubs
		#' @param exclude_grey
		#' @param
		#' @param n_hubs number of hub genes to use in the UMAP computation
		#' @param exclude_grey logical indicating whether to include grey module
		#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot
		#' @param ... Additional parameters supplied to uwot::umap
		#' @keywords scRNA-seq
		@@ -1629,7 +1628,7 @@ MotifTargetScore <- function(
		#' @examples
		RunModuleUMAP <- function(
		seurat_obj,
		n_hubs = 50,
		n_hubs = 10,
		exclude_grey = TRUE,
		wgcna_name = NULL,
		n_neighbors= 25,

R/getters_and_setters.R

+25 −1

Original line number	Diff line number	Diff line
		@@ -687,6 +687,17 @@ GetModuleTraitCorrelation <- function(seurat_obj, wgcna_name=NULL){
		# Reset module names:
		###########################


		#' ResetModuleNames
		#'
		#' Reset the uname of each scWGCNA module
		#'
		#' @param seurat_obj A Seurat object
		#' @param new_name string containing the base name to re-name the modules
		#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		ResetModuleNames <- function(
		seurat_obj,
		new_name = "M",
		@@ -820,6 +831,16 @@ ResetModuleNames <- function(
		# Reset module names:
		###########################

		#' ResetModuleColors
		#'
		#' Reset the unique color for each scWGCNA module
		#'
		#' @param seurat_obj A Seurat object
		#' @param new_colors a character vector containing the new colors
		#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		ResetModuleColors <- function(
		seurat_obj,
		new_colors,
		@@ -853,7 +874,6 @@ ResetModuleColors <- function(
		# set module table
		seurat_obj <- SetModules(seurat_obj, modules, wgcna_name)


		# update motif overlap
		overlap_df <- GetMotifOverlap(seurat_obj, wgcna_name)
		if(!is.null(overlap_df)){
		@@ -868,6 +888,10 @@ ResetModuleColors <- function(
		seurat_obj <- SetModuleUMAP(seurat_obj, umap_df, wgcna_name)
		}

		# update scWGCNA dendrogram:
		net <- GetNetworkData(seurat_obj, wgcna_name)
		net$colors <- new_color_df[match(net$colors, new_color_df$old),'new']
		seurat_obj <- SetNetworkData(seurat_obj, net, wgcna_name)

		seurat_obj

R/plotting.R

+2 −2

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		@@ -377,7 +377,7 @@ ModuleFeaturePlot<- function(
		ggplot(aes_string(x=x_name, y=y_name, color="val")) +
		# ggplot(aes(x=umap1, y=umap2, color=val))
		geom_point(size=point_size, alpha=alpha) +
		ggtitle(cur_mod) + umap_theme +
		ggtitle(cur_mod) + umap_theme() +
		labs(color="")

		# UCell?
		@@ -1508,7 +1508,7 @@ DoHubGeneHeatmap <- function(
		for(i in 1:nrow(mod_colors)){
		cbar_list[[i]] <- mod_colors[i,] %>% ggplot(aes(y=value, x=dummy)) +
		geom_bar(position='stack', stat='identity', fill=mod_colors[i,]$color) +
		umap_theme + theme(
		umap_theme() + theme(
		plot.margin=margin(0,0,0,0)
		)
		}

_pkgdown.yml

+9 −0

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		@@ -37,6 +37,10 @@ navbar:
		- text: Projecting modules onto new datasets
		href: articles/projecting_modules.html
		- text: -------
		- text: Other
		- text: Module customization
		href: articles/customization.html
		- text: -------
		- text: All vignettes
		href: articles/index.html

		@@ -75,6 +79,11 @@ reference:
		- '`RunHarmonyMetacells`'
		- '`RunUMAPMetacells`'
		- '`DimPlotMetacells`'
		- title: Other
		desc: Other functions
		contents:
		-'`ResetModuleColors`'
		-'`ResetModuleNames`'

		deploy:
		install_metadata: true

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