docstring for PlotKMEs/ (b8ef25b4) · Commits · github_fork / HdWGCNA

R/WGCNA_functions.R

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		@@ -813,6 +813,10 @@ ModuleConnectivity <- function(
		genes_use <- GetWGCNAGenes(seurat_obj, wgcna_name)
		params <- GetWGCNAParams(seurat_obj, wgcna_name)

		# exclude the grey module:
		#modules <- subset(modules, module != 'grey')
		#MEs <- MEs[,colnames(MEs) != 'grey']

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

		if(!is.null(group.by)){
		@@ -830,6 +834,8 @@ ModuleConnectivity <- function(
		)[genes_use,cells.use]

		datExpr <- t(as.matrix(exp_mat))
		print(dim(datExpr))
		print('running signedKME...')

		kMEs <- WGCNA::signedKME(
		datExpr,

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		@@ -1157,7 +1157,7 @@ ModuleUMAPPlot <- function(
		gene2 = as.character(edge_df[i,'Var2'])

		col1 <- selected_modules[selected_modules$gene_name == gene1, 'color']
		col2 <- selected_modules[sfelected_modules$gene_name == gene2, 'color']
		col2 <- selected_modules[selected_modules$gene_name == gene2, 'color']

		if(col1 == col2){
		col = col1

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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: 2022-05-09T17:14Z
		last_built: 2022-05-11T04:53Z
		urls:
		reference: https://smorabit.github.io/scWGCNA/reference
		article: https://smorabit.github.io/scWGCNA/articles

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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: 0x7fb69569ee40></span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7f94403e8d98></span>
		<span class="r-out co"><span class="r-pr">#></span> <environment: namespace:hdWGCNA></span>
		</code></pre></div>
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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: 0x7fb69bde9ca0></span>
		<span class="r-out co"><span class="r-pr">#></span> <bytecode: 0x7f94408191c8></span>
		<span class="r-out co"><span class="r-pr">#></span> <environment: namespace:hdWGCNA></span>
		</code></pre></div>
		</div>