working on pkgdown (93fd73d5) · Commits · github_fork / HdWGCNA

DESCRIPTION

+2 −1

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		@@ -13,4 +13,5 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to
		Encoding: UTF-8
		LazyData: true
		Roxygen: list(markdown = TRUE)
		RoxygenNote: 7.1.1
		RoxygenNote: 7.1.2
		URL: https://smorabit.github.io/scWGCNA/

+36 −0

Original line number	Diff line number	Diff line
		# Generated by roxygen2: do not edit by hand

		export(AvgModuleExpr)
		export(ComputeModuleEigengene)
		export(ComputeROC)
		export(ConstructMetacells)
		export(ConstructNetwork)
		export(DimPlotMetacells)
		export(EnrichrBarPlot)
		export(EnrichrDotPlot)
		export(GetDatExpr)
		export(GetMEs)
		export(HubGeneNetworkPlot)
		export(MetacellsByGroups)
		export(ModuleConnectivity)
		export(ModuleCorrNetwork)
		export(ModuleCorrelogram)
		export(ModuleEigengenes)
		export(ModuleExprScore)
		export(ModuleFeaturePlot)
		export(ModuleNetworkPlot)
		export(NormalizeMetacells)
		export(OverlapBarPlot)
		export(OverlapDotPlot)
		export(OverlapModulesDEGs)
		export(PlotDendrogram)
		export(ProjectModules)
		export(ROCCurves)
		export(RunEnrichr)
		export(RunHarmonyMetacells)
		export(RunPCAMetacells)
		export(RunUMAPMetacells)
		export(ScaleMetacells)
		export(SelectNetworkGenes)
		export(SetDatExpr)
		export(SetupForWGCNA)
		export(TestSoftPowers)
		export(TransferModuleGenome)
		export(construct_metacells)
		export(metacells_by_groups)

+11 −9

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		@@ -918,6 +918,7 @@ ComputeROC <- function(
		scale_genes=TRUE,
		verbose=FALSE,
		exp_thresh = 0.75,
		return_seurat=TRUE,
		wgcna_name=NULL, wgcna_name_test=NULL
		){

		@@ -975,7 +976,6 @@ ComputeROC <- function(

		}

		print('here')

		# get names of different cell groupings in test
		groups_test <- as.character(unique(Idents(seurat_test)))
		@@ -1010,13 +1010,6 @@ ComputeROC <- function(
		stop('Invalid feature selection. Valid choices: hMEs, MEs, scores.')
		)

		print('train')
		print(dim(MEs))
		print(dim(seurat_train))
		print('test')
		print(dim(MEs_p))
		print(dim(seurat_test))

		# add group column to MEs:
		MEs <- as.data.frame(MEs) %>% mutate(group = seurat_train@meta.data[[group.by]])
		MEs_p <- as.data.frame(MEs_p) %>% mutate(group = seurat_test@meta.data[[group.by]])
		@@ -1072,10 +1065,19 @@ ComputeROC <- function(
		colnames(conf_df)[1:3] <- c('lo', 'mid', 'hi')

		# return ROC tables & objects:
		list(
		roc_info = list(
		roc = plot_df,
		conf = conf_df,
		objects = roc_list
		)

		if(return_seurat){
		# add roc info to seurat object:
		seurat_obj <- SetROCData(seurat_obj, roc_info, wgcna_name)
		out <- seurat_obj
		} else{
		out <- roc_info
		}

		out
		}

+36 −0

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		@@ -381,6 +381,27 @@ GetTOM <- function(seurat_obj, wgcna_name=NULL){

		}

		############################
		# ROC Curve
		###########################

		SetROCData <- function(seurat_obj, roc_info, wgcna_name=NULL){

		# get data from active assay if wgcna_name is not given
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}
		seurat_obj@misc[[wgcna_name]]$roc_data <- roc_info
		seurat_obj
		}


		GetROCData <- function(seurat_obj, wgcna_name=NULL){

		# get data from active assay if wgcna_name is not given
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}
		seurat_obj@misc[[wgcna_name]]$roc_data
		}


		############################
		# Reset module names:
		###########################
		@@ -479,6 +500,21 @@ ResetModuleNames <- function(
		seurat_obj <- SetEnrichrTable(seurat_obj, enrich_table, wgcna_name)
		}

		# update ROC info:
		# THIS DOES NOT UPDATE THE ROC OBJECTS THEMSELVES!!!
		roc_data <- GetROCData(seurat_obj, wgcna_name)
		if(!is.na(roc_data)){
		roc_data$roc$module <- factor(
		new_mod_df[match(roc_data$roc$module, new_mod_df$old),'new'],
		levels = as.character(new_mod_df$new)
		)
		roc_data$conf$module <- factor(
		new_mod_df[match(roc_data$conf$module, new_mod_df$old),'new'],
		levels = as.character(new_mod_df$new)
		)
		seurat_obj <- SetROCData(seurat_obj, roc_data, wgcna_name)
		}

		seurat_obj

		}

+11 −7

Original line number	Diff line number	Diff line
		@@ -908,9 +908,7 @@ OverlapDotPlot <- function(
		p
		}

		#' OverlapBarPlot
		#'
		#' Makes barplots from Enrichr data
		#' Plots the results from OverlapModulesDEGs as a bar plot
		#'
		#' @param seurat_obj A Seurat object
		#' @param dbs List of EnrichR databases
		@@ -991,7 +989,7 @@ OverlapBarPlot <- function(
		#' ROCCurves
		ROCCurves <- function(
		seurat_obj,
		roc_df, conf_df, wgcna_name=NULL
		roc_df=NULL, conf_df=NULL, wgcna_name=NULL
		){

		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}
		@@ -1007,15 +1005,21 @@ ROCCurves <- function(
		distinct %>%
		arrange(module) %>% .$color

		# get the ROC info from seurat obj:
		if(is.null(roc_df) \| is.null(conf_df)){
		roc_df <- GetROCData(seurat_obj, wgcna_name)$roc
		conf_df <- GetROCData(seurat_obj, wgcna_name)$conf
		}

		# plot the ROC curve
		roc_df <- roc_df %>% group_by(module) %>% arrange(sensitivity)
		conf_df <- conf_df %>% group_by(module) %>% arrange(sensitivity)
		auc_df <- distinct(roc_df[,c('module', 'auc')])

		# set factor levels for modules:
		roc_df$module <- factor(roc_df$module, levels=mods)
		conf_df$module <- factor(conf_df$module, levels=mods)
		auc_df$module <- factor(auc_df$module, levels=mods)
		roc_df$module <- factor(as.character(roc_df$module), levels=mods)
		conf_df$module <- factor(as.character(conf_df$module), levels=mods)
		auc_df$module <- factor(as.character(auc_df$module), levels=mods)

		p <- roc_df %>% ggplot(
		aes(x=specificity, y=sensitivity, color=module, fill=module),