error check for selectnetworkgenes (16d72c0e) · Commits · github_fork / HdWGCNA

R/WGCNA_functions.R

+25 −2

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		@@ -15,7 +15,8 @@ SelectNetworkGenes <- function(
		seurat_obj,
		gene_select="variable", fraction=0.05,
		group.by=NULL, # should be a column in the Seurat object, eg clusters
		gene_list=NULL, wgcna_name=NULL
		gene_list=NULL,
		wgcna_name=NULL
		){

		# validate inputs:
		@@ -23,6 +24,14 @@ SelectNetworkGenes <- function(
		stop(paste0("Invalid selection gene_select: ", gene_select, '. Valid gene_selects are variable, fraction, all, or custom.'))
		}

		# get assay
		assay <- DefaultAssay(seurat_obj)
		tryCatch(
		tmp <- dim(seurat_obj[[assay]]@counts),
		error = function(e){
		print("Assay must contain counts slot.")
		})

		# handle different selection strategies
		if(gene_select == "fraction"){

		@@ -456,12 +465,24 @@ ComputeModuleEigengene <- function(

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

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

		# subset seurat object by these genes only:
		cur_seurat <- seurat_obj[cur_genes,]
		X <- GetAssayData(seurat_obj, slot='counts')[cur_genes,]
		X_dat <- GetAssayData(seurat_obj, slot='data')[cur_genes,]
		X_scaled <- GetAssayData(seurat_obj, slot='scale.data')[cur_genes,]
		cur_seurat <- CreateSeuratObject(X, assay = ass, meta.data = seurat_obj@meta.data)
		cur_seurat <- SetAssayData(cur_seurat, slot='data', new.data=X_dat, assay=ass)
		cur_seurat <- SetAssayData(cur_seurat, slot='scale.data', new.data=X_scaled, assay=ass)

		print(ass)
		print(head(cur_genes))
		# cur_seurat <- seurat_obj
		# cur_seurat[[ass]] <- cur_seurat[[ass]][cur_genes,]
		print('subset success')

		# scale the subsetted expression dataset:
		if(is.null(vars.to.regress)){
		@@ -472,6 +493,7 @@ ComputeModuleEigengene <- function(
		stop(paste0("Some variables specified in vars.to.regress are not found in seurat_obj@meta.data"))
		}


		# compute average expression of each gene
		cur_expr <- GetAssayData(cur_seurat, slot='data')
		expr <- t(as.matrix(cur_expr))
		@@ -619,6 +641,7 @@ ModuleEigengenes <- function(
		for(cur_mod in mods){

		print(cur_mod)
		print('here')

		# compute module eigengenes for this module
		seurat_obj <- ComputeModuleEigengene(

docs/pkgdown.yml

+1 −1

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		@@ -13,7 +13,7 @@ articles:
		network_visualizations: network_visualizations.html
		projecting_modules: projecting_modules.html
		projecting_modules_cross: projecting_modules_cross.html
		last_built: 2022-05-24T23:24Z
		last_built: 2022-06-03T00:21Z
		urls:
		reference: https://smorabit.github.io/scWGCNA/reference
		article: https://smorabit.github.io/scWGCNA/articles

docs/reference/ComputeROC.html

+1 −1

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		@@ -234,7 +234,7 @@
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> out</span>
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7faaeb538c38></span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7fc3084faf60></span>
		<span class="r-out co"><span class="r-pr">#></span> <environment: namespace:hdWGCNA></span>
		</code></pre></div>
		</div>

docs/reference/DoHubGeneHeatmap.html

+1 −1

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		@@ -221,7 +221,7 @@ using Seurat's DoHeatmap, and then assembles them all into one big heatmap.</p>
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> out</span>
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7faaeb216c38></span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7fc30aa4cd80></span>
		<span class="r-out co"><span class="r-pr">#></span> <environment: namespace:hdWGCNA></span>
		</code></pre></div>
		</div>

docs/reference/EnrichrBarPlot.html

+1 −1

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		@@ -195,7 +195,7 @@
		<span class="r-out co"><span class="r-pr">#></span> dev.off()</span>
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> }</span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7faaec252890></span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7fc305eab288></span>
		<span class="r-out co"><span class="r-pr">#></span> <environment: namespace:hdWGCNA></span>
		</code></pre></div>
		</div>

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