added consensus tutorial (e926942b) · Commits · github_fork / HdWGCNA

DESCRIPTION

+1 −1

Original line number	Diff line number	Diff line
		Package: hdWGCNA
		Title: hdWGCNA
		Version: 0.1.1.9006
		Version: 0.1.1.9008
		Authors@R: c(
		person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0002-7768-4856")),

NEWS.md

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Original line number	Diff line number	Diff line
		# hdWGCNA 0.1.1.9008 (2022-07-21)
		## Added
		- New tutorial for consensus co-expression network analysis.

		## Changes
		- `ModuleNetworkPlot` and `RunModuleUMAP` now checks if `ModuleConnectivity` has been computed in order to throw a more informative error.
		- `GetTOM` checks if the TOM file exists in order to throw a more informative error.


		# hdWGCNA 0.1.1.9007 (2022-07-20)
		## Added
		- None

R/WGCNA_functions.R

+40 −19

Original line number	Diff line number	Diff line
		@@ -174,7 +174,7 @@ SetupForWGCNA <- function(
		TestSoftPowers <- function(
		seurat_obj,
		powers=c(seq(1,10,by=1), seq(12,30, by=2)),
		setDatExpr = TRUE,
		setDatExpr = FALSE,
		use_metacells = TRUE,
		group.by=NULL, group_name=NULL
		){
		@@ -221,7 +221,7 @@ TestSoftPowers <- function(
		TestSoftPowersConsensus <- function(
		seurat_obj,
		powers=c(seq(1,10,by=1), seq(12,30, by=2)),
		setDatExpr = TRUE,
		setDatExpr = FALSE,
		use_metacells = TRUE,
		group.by=NULL, group_name=NULL,
		multi.group.by = NULL,
		@@ -291,7 +291,7 @@ ConstructNetwork <- function(
		seurat_obj, soft_power=NULL, min_power=3,
		tom_outdir="TOM",
		use_metacells=TRUE,
		setDatExpr=TRUE, group.by=NULL,
		setDatExpr=FALSE, group.by=NULL,
		group_name=NULL,
		tom_name = NULL,
		consensus = FALSE,
		@@ -309,6 +309,22 @@ ConstructNetwork <- function(

		wgcna_name <- seurat_obj@misc$active_wgcna


		# suffix for the tom
		if(is.null(tom_name)){
		tom_name <- gsub(' ', '_', group_name)
		}

		# tom file name
		renamed <- paste0(tom_outdir, '/', tom_name, '_TOM.rda')
		if(file.exists(renamed)){
		if(overwrite_tom){
		warning(paste0('Overwriting TOM ', renamed))
		} else{
		stop(paste0("TOM ", renamed, " already exists. Set overwrite_tom = TRUE or change tom_name to proceed."))
		}
		}

		# constructing network on multiple datasets (consensus WGCNA)
		if(consensus){

		@@ -349,21 +365,21 @@ ConstructNetwork <- function(
		if(is.null(group_name)){
		group_name <- 'all'
		}

		# suffix for the tom
		if(is.null(tom_name)){
		tom_name <- gsub(' ', '_', group_name)
		}

		# tom file name
		renamed <- paste0(tom_outdir, '/', tom_name, '_TOM.rda')
		if(file.exists(renamed)){
		if(overwrite_tom){
		warning(paste0('Overwriting TOM ', renamed))
		} else{
		stop(paste0("TOM ", renamed, " already exists. Set overwrite_tom = TRUE or change tom_name to proceed."))
		}
		}
		#
		# # suffix for the tom
		# if(is.null(tom_name)){
		# tom_name <- gsub(' ', '_', group_name)
		# }
		#
		# # tom file name
		# renamed <- paste0(tom_outdir, '/', tom_name, '_TOM.rda')
		# if(file.exists(renamed)){
		# if(overwrite_tom){
		# warning(paste0('Overwriting TOM ', renamed))
		# } else{
		# stop(paste0("TOM ", renamed, " already exists. Set overwrite_tom = TRUE or change tom_name to proceed."))
		# }
		# }

		nSets = 1
		setLabels = gsub(' ', '_', group_name)
		@@ -898,7 +914,7 @@ ModuleConnectivity <- function(
		#modules <- subset(modules, module != 'grey')
		#MEs <- MEs[,colnames(MEs) != 'grey']

		if(is.null(assay)){assay <- seurat_obj@active.assay}
		if(is.null(assay)){assay <- DefaultAssay(seurat_obj)}

		if(!is.null(group.by)){
		cells.use <- seurat_obj@meta.data %>% subset(get(group.by) %in% group_name) %>% rownames
		@@ -1673,6 +1689,11 @@ RunModuleUMAP <- function(
		modules <- GetModules(seurat_obj, wgcna_name)
		mods <- levels(modules$module)

		# check if we have eigengene-based connectivities:
		if(!all(paste0('kME_', as.character(mods)) %in% colnames(modules))){
		stop('Eigengene-based connectivity (kME) not found. Did you run ModuleEigengenes and ModuleConnectivity?')
		}

		if(exclude_grey){
		mods <- mods[mods != 'grey']
		modules <- subset(modules, module != 'grey')

R/getters_and_setters.R

+32 −8

Original line number	Diff line number	Diff line
		@@ -197,11 +197,6 @@ SetDatExpr <- function(
		genes_use <- GetWGCNAGenes(seurat_obj, wgcna_name)
		modules <- GetModules(seurat_obj, wgcna_name)

		if(is.null(assay)){
		assay <- params$metacell_assay
		warning(paste0('assay not specified, trying to use assay ', assay))
		}

		# use metacells or whole seurat object?
		if(use_metacells){
		s_obj <- GetMetacellObject(seurat_obj, wgcna_name)
		@@ -209,6 +204,12 @@ SetDatExpr <- function(
		s_obj <- seurat_obj
		}


		if(is.null(assay)){
		assay <- DefaultAssay(s_obj)
		warning(paste0('assay not specified, trying to use assay ', assay))
		}

		# check the assay:
		if(!(assay %in% names(s_obj@assays))){
		stop("Assay not found. Check names(seurat_obj@assays) or names(GetMetacellObject(seurat_obj)@assays)")
		@@ -257,7 +258,6 @@ SetDatExpr <- function(
		datExpr <- datExpr[,gene_list]
		}


		if(return_seurat){

		# update the WGCNA gene list:
		@@ -301,7 +301,7 @@ GetDatExpr <- function(seurat_obj, wgcna_name=NULL){
		#' @param use_metacells A logical determining if we use the metacells (TRUE) or the full expression matrix (FALSE)
		#' @param group.by A string containing the name of a column in the Seurat object with cell groups (clusters, cell types, etc). If NULL (default), hdWGCNA uses the Seurat Idents as the group.
		#' @param multi.group.by A string containing the name of a column in the Seurat object with groups for consensus WGCNA (dataset, sample, condition, etc)
		#' @param multi_groups A character vecrtor containing the names of
		#' @param multi_groups A character vecrtor containing the names of groups to select
		#' @param wgcna_name A string containing the name of the WGCNA slot in seurat_obj@misc. Default = NULL which retrieves the currently active WGCNA data
		#' @keywords scRNA-seq
		#' @export
		@@ -315,6 +315,8 @@ SetMultiExpr <- function(
		multi.group.by = NULL,
		multi_groups = NULL,
		wgcna_name=NULL,
		assay=NULL,
		slot='data',
		...
		){

		@@ -322,8 +324,22 @@ SetMultiExpr <- function(
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

		# get the WGCNA genes:
		params <- GetWGCNAParams(seurat_obj, wgcna_name)
		gene_names <- GetWGCNAGenes(seurat_obj, wgcna_name)

		# use metacells or whole seurat object?
		if(use_metacells){
		s_obj <- GetMetacellObject(seurat_obj, wgcna_name)
		} else{
		s_obj <- seurat_obj
		}

		# get assay
		if(is.null(assay)){
		assay <- DefaultAssay(s_obj)
		warning(paste0('assay not specified, trying to use assay ', assay))
		}

		# get the different groups present if not specified by the user:
		if(is.null(multi_groups)){
		multi_groups <- unique(seurat_obj@meta.data[[multi.group.by]])
		@@ -343,7 +359,10 @@ SetMultiExpr <- function(
		multi.group.by = multi.group.by,
		multi_group_name = x,
		return_seurat = FALSE,
		wgcna_name = wgcna_name
		use_metacells = use_metacells,
		wgcna_name = wgcna_name,
		assay = assay,
		slot = slot
		) %>% as.matrix
		})
		datExpr_list
		@@ -804,6 +823,11 @@ GetTOM <- function(seurat_obj, wgcna_name=NULL){

		# load TOM
		tom_files <- GetNetworkData(seurat_obj, wgcna_name)$TOMFiles

		if(!file.exists(tom_files[[1]])){
		stop(paste0("TOM file ", tom_files[[1]], ' not found. Please update path to TOM file.'))
		}

		load(tom_files[[1]])

		TOM <- as.matrix(consTomDS)

R/plotting.R

+10 −1

Original line number	Diff line number	Diff line
		@@ -572,7 +572,9 @@ ModuleFeaturePlot<- function(
		}

		# aspect ratio:
		if(is.numeric(plot_ratio)){
		p <- p + coord_fixed(ratio = plot_ratio)
		}

		# UCell?
		if(!ucell){
		@@ -834,12 +836,19 @@ ModuleNetworkPlot <- function(
		MEs <- GetMEs(seurat_obj, wgcna_name)
		modules <- GetModules(seurat_obj, wgcna_name)



		# using all modules?
		if(mods == 'all'){
		mods <- levels(modules$module)
		mods <- mods[mods != 'grey']
		}

		# check if we have eigengene-based connectivities:
		if(!all(paste0('kME_', as.character(mods)) %in% colnames(modules))){
		stop('Eigengene-based connectivity (kME) not found. Did you run ModuleEigengenes and ModuleConnectivity?')
		}

		# create output folder
		if(!dir.exists(outdir)){dir.create(outdir)}

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