kME function and plotting function (c78a7f29) · Commits · github_fork / HdWGCNA

R/WGCNA_functions.R

+50 −1

Original line number	Diff line number	Diff line
		@@ -380,6 +380,24 @@ ModuleEigengenes <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, ...){
		seurat_obj
		}

		#' GetMEs
		#'
		#' Function to retrieve module eigengens from Seurat object.
		#'
		#' @param seurat_obj A Seurat object
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' ModuleEigengenes(pbmc)
		GetMEs <- function(seurat_obj, harmonized=TRUE){
		if(harmonized == TRUE && !is.null(seurat_obj@misc$wgcna_hMEs)){
		MEs <- seurat_obj@misc$wgcna_hMEs
		} else{
		MEs <- seurat_obj@misc$wgcna_MEs
		}
		MEs
		}


		#' ModuleConnectivity
		#'
		@@ -390,6 +408,37 @@ ModuleEigengenes <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, ...){
		#' @export
		#' @examples
		#' ModuleConnectivity(pbmc)
		ModuleConnectivity <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, ...){
		ModuleConnectivity <- function(seurat_obj, harmonized=TRUE, ...){

		# get expression matrix
		genes_use <- names(seurat_obj@misc$wgcna_net$colors)

		# datExpr for full expression dataset
		# transpose expression data and subset by genes used for WGCNA
		datExpr <- t(GetAssayData(
		seurat_obj,
		assay=seurat_obj@misc$wgcna_params$metacell_assay,
		slot=seurat_obj@misc$wgcna_params$metacell_slot
		))[,genes_use]

		# get MEs:
		MEs <- GetMEs(seurat_obj=seurat_obj, harmonized=harmonized)

		tic("SignedKME")
		kMEs <- signedKME(
		datExpr,
		MEs,
		outputColumnName = "kME",
		corFnc = "bicor",
		...
		)
		toc()

		# add module color to the kMEs table
		kMEs <- cbind(cur_seurat@misc$wgcna_net$colors, kMEs)
		colnames(kMEs) <- c('module', colnames(MEs))

		seurat_obj@misc$wgcna_kMEs <- kMEs
		seurat_obj

		}

R/plotting.R

0 → 100644

+109 −0

Original line number	Diff line number	Diff line

		#' PlotDendrogram
		#'
		#' Plot WGCNA dendrogram
		#'
		#' @param seurat_obj A Seurat object
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' PlotDendrogram
		PlotDendrogram <- function(
		seurat_obj, groupLabels="Module colors",
		dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05,
		main = "", ...
		){

		WGCNA::plotDendroAndColors(
		seurat_obj@misc$wgcna_net$dendrograms[[1]],
		as.character(seurat_obj@misc$wgcna_net$colors),
		groupLabels=groupLabels,
		dendroLabels = dendroLabels,
		hang = hang,
		addGuide = addGuide,
		guideHang = guideHang,
		main = main,
		...
		)
		}


		#' MEFeaturePlot
		#'
		#' Plot module eigengenes as a FeaturePlot
		#'
		#' @param seurat_obj A Seurat object
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' MEFeaturePlot
		MEFeaturePlot<- function(
		seurat_obj, modules,
		harmonized=TRUE, reduction='umap',
		order=TRUE, restrict_range=TRUE, point_size = 0.5,
		label_legend = FALSE
		){

		# get MEs from seurat object
		MEs <- GetMEs(seurat_obj, harmonized)

		# get reduction from seurat obj
		umap <- seurat_obj@reductions[[reduction]]@cell.embeddings
		x_name <- colnames(umap)[1]
		y_name <- colnames(umap)[2]

		# merge into one df for plotting
		plot_df <- cbind(umap, MEs) %>% as.data.frame()

		plot_list <- list()
		for(cur_mod in modules){

		cur_color <- cur_mod

		# reset the range of the plot:
		plot_range <- plot_df[,cur_mod] %>% range
		if(restrict_range){
		if(abs(plot_range[1]) > abs(plot_range[2])){
		plot_range[1] <- -1*plot_range[2]
		} else{
		plot_range[2] <- -1*plot_range[1]
		}
		plot_df[,cur_mod] <- ifelse(plot_df[,cur_mod] > plot_range[2], plot_range[2], plot_df[,cur_mod])
		plot_df[,cur_mod] <- ifelse(plot_df[,cur_mod] < plot_range[1], plot_range[1], plot_df[,cur_mod])
		}

		# order points:
		if(order){
		plot_df <- plot_df %>% dplyr::arrange_(cur_mod)
		}

		# label for plot:
		if(harmonized){
		label <- paste0('hME_', cur_mod)
		} else{
		label <- paste0('ME_', cur_mod)
		}

		# plot with ggplot
		plot_list[[cur_mod]] <- plot_df %>%
		ggplot(aes_string(x=x_name, y=y_name, color=cur_mod)) +
		geom_point(size=0.5) +
		scale_color_gradient2(
		low='grey75', mid='grey95', high=cur_color,
		breaks = c(plot_range[1], 0, plot_range[2]),
		labels = c('-', '0', '+'),
		) +
		ggtitle(label) + umap_theme +
		labs(color="")
		}

		# return plot
		if(length(plot_list) == 1){
		p <- plot_list[[1]]
		} else{
		p <- plot_list
		}

		p

		}

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