network vis tutorial (bef3e8d0) · Commits · github_fork / HdWGCNA

R/WGCNA_functions.R

+23 −8

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		@@ -1625,6 +1625,7 @@ RunModuleUMAP <- function(
		metric = "cosine",
		spread=1,
		min_dist=0.4,
		supervised = FALSE,
		...
		){

		@@ -1658,14 +1659,28 @@ RunModuleUMAP <- function(
		umap_TOM <- TOM[selected_genes,unlist(hub_list)]

		# run UMAP
		if(supervised){
		print('running supervised UMAP:')
		hub_umap <- uwot::umap(
		X = umap_TOM,
		min_dist = min_dist,
		n_neighbors= n_neighbors,
		metric = metric,
		spread=spread,
		y = modules$module, # for supervised UMAP
		...
		)
		} else {
		hub_umap <- uwot::umap(
		X = umap_TOM,
		min_dist = min_dist,
		n_neighbors= n_neighbors,
		metric = metric,
		spread=spread,
		...
		)
		}


		# set up plotting df
		plot_df <- as.data.frame(hub_umap)

+17 −0

Original line number	Diff line number	Diff line
		@@ -3,3 +3,20 @@ scale01 <- function(x){
		y <- min(x); z <- max(x);
		(x-y) / (z-y)
		}

		umap_theme <- function(){
		theme(
		axis.line=element_blank(),
		axis.text.x=element_blank(),
		axis.text.y=element_blank(),
		axis.ticks=element_blank(),
		axis.title.x=element_blank(),
		axis.title.y=element_blank(),
		panel.background=element_blank(),
		panel.border=element_blank(),
		panel.grid.major=element_blank(),
		panel.grid.minor=element_blank(),
		plot.background=element_blank(),
		plot.title = element_text(hjust = 0.5)
		)
		}

+1 −1

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		@@ -758,7 +758,7 @@ HubGeneNetworkPlot <- function(
		return_graph=FALSE,
		edge.alpha=0.25,
		vertex.label.cex=0.5,
		hub.vertex.size=4,
		hub.vertex.size=4,Ω
		other.vertex.size=1,
		wgcna_name=NULL,
		...

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+1.32 MiB

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+268 KiB

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