Class: Net_plotter

Inherits:
Object
  • Object
show all
Defined in:
lib/NetAnalyzer/net_plotter.rb

Instance Method Summary collapse

Constructor Details

#initialize(net_data, options = {}) ⇒ Net_plotter

Returns a new instance of Net_plotter.



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# File 'lib/NetAnalyzer/net_plotter.rb', line 13

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

Instance Method Details

#cyt_app_add_edges(node_ids, count) ⇒ Object 



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# File 'lib/NetAnalyzer/net_plotter.rb', line 85

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

#cyt_app_add_node(nodes, count, node, group_nodes) ⇒ Object 



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# File 'lib/NetAnalyzer/net_plotter.rb', line 65

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

#plot_cyt_app(user_options = {}) ⇒ Object 



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# File 'lib/NetAnalyzer/net_plotter.rb', line 37

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

#plot_dot(user_options = {}) ⇒ Object

input keys: layout



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# File 'lib/NetAnalyzer/net_plotter.rb', line 109

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