changed install instructions (757542fb) · Commits · github_fork / HdWGCNA

R/plotting.R

+11 −4

Original line number	Diff line number	Diff line
		@@ -1102,6 +1102,7 @@ ModuleUMAPPlot <- function(
		label_hubs = 5, # how many hub genes to label?
		edge.alpha=0.25,
		vertex.label.cex=0.5,
		label_genes = NULL,
		return_graph = FALSE, # this returns the igraph object instead of plotting
		wgcna_name=NULL,
		...
		@@ -1126,8 +1127,16 @@ ModuleUMAPPlot <- function(
		# subset the TOM:
		subset_TOM <- TOM[umap_df$gene, umap_df$gene[umap_df$hub == 'hub']]

		# labels
		label_genes <- selected_modules %>% group_by(module) %>% top_n(label_hubs, wt=kME) %>% .$gene_name
		# genes to label:
		hub_labels <- selected_modules %>% group_by(module) %>% top_n(label_hubs, wt=kME) %>% .$gene_name
		if(is.null(label_genes)){
		label_genes <- hub_labels
		} else{
		if(!any(label_genes %in% umap_df$gene)){
		stop("Some genes in label_genes not found in the UMAP.")
		}
		label_genes <- unique(c(label_genes, hub_labels))
		}
		selected_modules$label <- ifelse(selected_modules$gene_name %in% label_genes, selected_modules$gene_name, '')
		selected_modules$fontcolor <- ifelse(selected_modules$color == 'black', 'gray50', 'black')

		@@ -1157,9 +1166,7 @@ ModuleUMAPPlot <- function(

		# subset edges:
		groups <- unique(edge_df$color)
		print(groups)
		if(sample_edges){
		print('here')
		# randomly sample
		temp <- do.call(rbind, lapply(groups, function(cur_group){
		cur_df <- edge_df %>% subset(color == cur_group)

+1 −1

Original line number	Diff line number	Diff line
		@@ -50,5 +50,5 @@ install.packages(c("Seurat", "WGCNA", "igraph", "devtools"))
		Now you can install the scWGCNA package using `devtools`.

		```r
		devtools::install_github('smorabit/scWGCNA', branch='dev')
		devtools::install_github('smorabit/scWGCNA', ref='dev')
		```

+1 −1

Original line number	Diff line number	Diff line
		@@ -163,7 +163,7 @@
		<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Seurat"</span>, <span class="st">"WGCNA"</span>, <span class="st">"igraph"</span>, <span class="st">"devtools"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
		<p>Now you can install the scWGCNA package using <code>devtools</code>.</p>
		<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
		<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">'smorabit/scWGCNA'</span>, branch<span class="op">=</span><span class="st">'dev'</span><span class="op">)</span></code></pre></div>
		<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">'smorabit/scWGCNA'</span>, ref<span class="op">=</span><span class="st">'dev'</span><span class="op">)</span></code></pre></div>
		</div>
		</div>
		</div>