working on module projection code (922e0410) · Commits · github_fork / HdWGCNA

R/WGCNA_functions.R

+27 −11

Original line number	Diff line number	Diff line
		@@ -76,21 +76,28 @@ SelectNetworkGenes <- function(seurat_obj, gene_select="variable", fraction=0.05
		#' @export
		#' @examples
		#' SetupForWGCNA(pbmc)
		SetupForWGCNA <- function(seurat_obj, wgcna_name, group=NULL, ...){
		SetupForWGCNA <- function(
		seurat_obj, wgcna_name,
		group=NULL, features = NULL,...){

		# set the active WGCNA variable
		seurat_obj <- SetActiveWGCNA(seurat_obj, wgcna_name)

		# set the active WGCNA group, this is used for actually
		# making the co-expression network
		# TODO: I never actually use WGCNAGroup anywhere??
		if(is.null(group)){
		seurat_obj <- SetWGCNAGroup(seurat_obj, group='all', wgcna_name)
		} else{
		seurat_obj <- SetWGCNAGroup(seurat_obj, group, wgcna_name)
		}

		# select genes for WGCNA:
		seurat_obj <- SelectNetworkGenes(seurat_obj, ...)
		# select genes for WGCNA, else use pre-selected:
		if(is.null(features)){
		seurat_obj <- SelectNetworkGenes(seurat_obj, wgcna_name=wgcna_name, ...)
		} else{
		seurat_obj <- SetWGCNAGenes(seurat_obj, gene_list=features, wgcna_name=wgcna_name)
		}

		seurat_obj
		}
		@@ -305,14 +312,15 @@ ConstructNetwork <- function(
		#' @export
		#' @examples
		#' ConstructNetwork(pbmc)
		ComputeModuleEigengene <- function(seurat_obj, cur_mod, group.by.vars=NULL, verbose=TRUE, wgcna_name=NULL, ...){
		ComputeModuleEigengene <- function(
		seurat_obj, cur_mod, modules,
		group.by.vars=NULL, verbose=TRUE,
		wgcna_name=NULL, ...
		){

		# set as active assay if wgcna_name is not given
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

		# get module df:
		modules <- GetModules(seurat_obj, wgcna_name)

		# get genes in this module:
		cur_genes <- modules %>% subset(module == cur_mod) %>% .$gene_name

		@@ -359,7 +367,11 @@ ComputeModuleEigengene <- function(seurat_obj, cur_mod, group.by.vars=NULL, verb
		#' @export
		#' @examples
		#' ModuleEigengenes(pbmc)
		ModuleEigengenes <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, wgcna_name=NULL, ...){
		ModuleEigengenes <- function(
		seurat_obj, group.by.vars=NULL,
		modules=NULL, verbose=TRUE,
		wgcna_name=NULL, ...
		){

		# set as active assay if wgcna_name is not given
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}
		@@ -369,7 +381,11 @@ ModuleEigengenes <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, wgcna

		me_list <- list()
		harmonized_me_list <- list()

		# get modules from Seurat object, else use provided modules
		if(is.null(modules)){
		modules <- GetModules(seurat_obj, wgcna_name)
		}

		# loop over modules:
		for(cur_mod in unique(modules$module)){
		@@ -379,8 +395,8 @@ ModuleEigengenes <- function(seurat_obj, group.by.vars=NULL, verbose=TRUE, wgcna
		# compute module eigengenes for this module
		seurat_obj <- ComputeModuleEigengene(
		seurat_obj = seurat_obj, cur_mod = cur_mod,
		group.by.vars=group.by.vars, verbose=verbose,
		wgcna_name, ...
		modules=modules, group.by.vars=group.by.vars, verbose=verbose,
		wgcna_name=wgcna_name, ...
		)

		# add module eigengene to ongoing list

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