NetAnalyzer 0.6.2 → 0.6.3

data/lib/NetAnalyzer/net_plotter.rb

@@ -0,0 +1,145 @@
+require 'gv'
+
+#For javascrip plotting
+require 'erb'
+require 'base64'
+require 'json'
+require 'zlib'
+
+TEMPLATES = File.join(File.dirname(__FILE__), 'templates')
+
+
+class Net_plotter
+	def initialize(net_data, options = {})
+		@group_nodes = net_data[:group_nodes]
+		@reference_nodes = net_data[:reference_nodes]
+		@nodes = net_data[:nodes]
+		@edges = net_data[:edges]
+		@layers = net_data[:layers]
+
+		if options[:method] == 'graphviz'
+			plot_dot(options)
+		elsif options[:method] == 'cyt_app'
+			plot_cyt_app(options)
+		else
+			if options[:method] == 'elgrapho'
+				template = 'el_grapho'
+			elsif options[:method] == 'cytoscape'
+				template = 'cytoscape'
+			elsif options[:method] == 'sigma'
+				template = 'sigma'
+			end
+			renderered_template = ERB.new(File.open(File.join(TEMPLATES, template + '.erb')).read).result(binding)
+			File.open(options[:output_file] + '.html', 'w'){|f| f.puts renderered_template}
+		end	
+	end
+
+	def plot_cyt_app(user_options = {})
+		options = {}
+		options = options.merge(user_options)
+
+		node_cyt_ids = {}
+		nodes = []
+		count = 0
+		group_nodes = {}
+		@group_nodes.each do |groupID, gNodes|
+			gNodes.each do |gNode|
+				group_nodes[gNode] = groupID
+			end
+		end
+		@nodes.each do |id, node|
+			cyt_app_add_node(nodes, count, node, group_nodes)
+			node_cyt_ids[id] = count.to_s
+			count += 1
+		end
+		edges = cyt_app_add_edges(node_cyt_ids, count)
+		cys_net = {
+			'elements' => {
+				'nodes' => nodes,
+				'edges' => edges
+			}
+		}
+		File.open(options[:output_file]+ '.cyjs', 'w'){|f| f.print JSON.pretty_generate(cys_net)}
+	end
+
+	def cyt_app_add_node(nodes, count, node, group_nodes)
+		id = node.id
+		cyt_node = {
+			'data' => {
+				'id' => count.to_s,
+				'name' => id
+			}
+		}
+		cyt_node['data']['type'] = node.type
+		if !@reference_nodes.empty?
+			ref = @reference_nodes.include?(id) ? 'y' : 'n'
+			cyt_node['data']['ref'] = ref
+		end
+		if !group_nodes.empty?
+			query = group_nodes[id]
+			cyt_node['data']['group'] = query if !query.nil?			
+		end
+		nodes << cyt_node
+	end
+
+	def cyt_app_add_edges(node_ids, count)
+		edges = []
+		plotted_edges = {}
+		@edges.each do |nodeID, associatedIDs|
+			associatedIDs.each do |associatedID|
+				pair = [nodeID, associatedID].sort.join('_').to_sym
+				if !plotted_edges[pair]
+					edges << {
+						'data' => {
+							'id' => count.to_s,
+							'source' => node_ids[nodeID],
+							'target' => node_ids[associatedID],
+							"interaction" => "-",
+							"weight" => 1.0
+						}
+					}
+					count +=1
+					plotted_edges[pair] = true
+				end
+			end
+		end
+		return edges
+	end
+
+	def plot_dot(user_options = {}) # input keys: layout
+		options = {layout: "sfdp"}
+		options = options.merge(user_options)
+		graphviz_colors = %w[lightsteelblue1 lightyellow1 lightgray orchid2]
+		palette = {}
+		@layers.each do |layer|
+			palette[layer] = graphviz_colors.shift
+		end
+		graph = GV::Graph.open('g', type = :undirected)
+		plotted_edges = {}
+		@edges.each do |nodeID, associatedIDs|
+			associatedIDs.each do |associatedID|
+				pair = [nodeID, associatedID].sort.join('_').to_sym
+				if !plotted_edges[pair]
+					graph.edge 'e', 
+						graph.node(nodeID, label: '', style: 'filled', fillcolor: palette[@nodes[nodeID].type]), 
+						graph.node(associatedID, label: '', style: 'filled' , fillcolor: palette[@nodes[associatedID].type])
+					plotted_edges[pair] = true
+				end
+			end
+		end
+		@reference_nodes.each do |nodeID|
+			graph.node(nodeID, style: 'filled', fillcolor: 'firebrick1', label: '')
+		end
+		graphviz_border_colors = %w[blue darkorange red olivedrab4]
+		@group_nodes.each do |groupID, gNodes|
+			border_color = graphviz_border_colors.shift
+			gNodes.each do |nodeID|
+					graph.node(nodeID, color: border_color, penwidth: '10', label: '')
+			end
+		end
+		graph[:overlap] = false
+		STDERR.puts 'Save graph'
+		graph.save(options[:output_file] + '.png', format='png', layout=options[:layout])
+	end
+
+end