Class: Bio::Assembly::ABVisualiser

Inherits:
Object
  • Object
show all
Includes:
FinishM::Logging
Defined in:
lib/assembly/a_b_visualiser.rb

Defined Under Namespace

Classes: SimplifiedGraph

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#graphviz(graph, options = {}) ⇒ Object

Visualise a (velvet) graph, as a graphviz object

Possible options: :start_kmers: list of kmers to denote the start node(s) :end_kmers: list of kmers to denote the end node(s) :start_node_id: ID of node to mark as a start :end_node_id:ID of node to mark as a end :start_node_ids: array of node IDs to mark as a start :end_node_ids:array of node IDs to mark as a end :coverage_cutoff: ignore nodes with less coverage than this cutoff :digraph: output as a digraph (default true, else output undirected graph) :nodes: an Enumerable of nodes to be visualised. :node_id_to_nickname: add these names to the node descriptions. Hash of integer node id to String. :paired_nodes_hash: a hash of node_id to Enumerable of node_ids where there is paired-end connections



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# File 'lib/assembly/a_b_visualiser.rb', line 32

def graphviz(graph, options={})
  opts = {}
  opts[:type] = :digraph unless options[:digraph] == false
  opts[:overlap] = :scale
  graphviz = GraphViz.new(:G, opts)

  nodes_to_explore = Set.new(options[:nodes].to_a)
  nodes_to_explore ||= Set.new(graph.nodes)

  # Add all the nodes
  blacklisted_node_ids = Set.new
  log.debug "Converting nodes to GraphViz format"
  nodes_to_explore.each do |node|
    cov = node.coverage
    if options[:coverage_cutoff] and cov < options[:coverage_cutoff] and !cov.nil?
      blacklisted_node_ids.add node.node_id
    else
      cov_string = cov.nil? ? '' : cov.round
      label = "n#{node.node_id}_length#{node.ends_of_kmers_of_node.length}_coverage#{cov_string}"
      if options[:node_id_to_nickname] and options[:node_id_to_nickname].key?(node.node_id)
        label += ' ' + options[:node_id_to_nickname][node.node_id]
      end
      mods = {
        :label => label,
      }
      includes_start = false
      includes_end = false
      if options[:start_kmers]
        includes_start = node.includes_kmers?(options[:start_kmers])
      end
      if options[:end_kmers]
        includes_end = node.includes_kmers?(options[:end_kmers])
      end
      if options[:start_node_id]
        includes_start = true if node.node_id == options[:start_node_id]
      end
      if options[:end_node_id]
        includes_end = true if node.node_id == options[:end_node_id]
      end
      if options[:start_node_ids]
        includes_start = true if options[:start_node_ids].include? node.node_id
      end
      if options[:end_node_ids]
        includes_end = true if options[:end_node_ids].include? node.node_id
      end

      if includes_start and includes_end
        log.warn "Start and end kmers detected in the same node!"
      elsif includes_start
        mods[:color] = "red"
      elsif includes_end
        mods[:color] = "green"
      end

      graphviz.add_nodes node.node_id.to_s, mods
    end
  end

  # Add all the edges
  arcs_of_interest = graph.arcs
  if options[:nodes]
    arcs_of_interest = Set.new
    nodes_to_explore.each do |node|
      graph.arcs.get_arcs_by_node_id(node.node_id).each do |arc|
        arcs_of_interest << arc
      end
    end
  end

  log.info "Converting #{arcs_of_interest.length} arcs to GraphViz format"
  arcs_of_interest.each do |arc|
    # Add unless the node has been blacklisted
    unless blacklisted_node_ids.include? arc.begin_node_id or
      blacklisted_node_ids.include? arc.end_node_id or
      !nodes_to_explore.include?(graph.nodes[arc.begin_node_id]) or
      !nodes_to_explore.include?(graph.nodes[arc.end_node_id])

      # Direction of the arrows, to denote connection to beginning of node (connects to start = in-arrow-head to node on output graph)
      if arc.connects_end_to_beginning?(arc.begin_node_id, arc.end_node_id)
        graphviz.add_edges arc.begin_node_id.to_s, arc.end_node_id.to_s
      elsif  arc.connects_end_to_end?(arc.begin_node_id, arc.end_node_id)
        graphviz.add_edges arc.begin_node_id.to_s, arc.end_node_id.to_s, {:dir => "none"}
      elsif  arc.connects_beginning_to_beginning?(arc.begin_node_id, arc.end_node_id)
        graphviz.add_edges arc.begin_node_id.to_s, arc.end_node_id.to_s, {:dir => "both"}
      elsif  arc.connects_beginning_to_end?(arc.begin_node_id, arc.end_node_id)
        graphviz.add_edges arc.end_node_id.to_s, arc.begin_node_id.to_s
      end
    end
  end

  # Add paired_nodes_hash pairs
  unless options[:paired_nodes_hash].nil?
    # Create a list of arc node pairs for len calculation
    arc_pairs = arcs_of_interest.collect do |arc|
      [arc.begin_node_id, arc.end_node_id].sort
    end
    directly_connected_node_pairs = Set.new(arc_pairs)

    # Keep track of pairs so multiple arcs are not drawn e.g. node1 => node2 and node2=>node1
    pairs_added = Set.new
    log.info "Adding paired-end linkages to GraphViz format.."
    options[:paired_nodes_hash].each do |node1_id, connected_node_ids|
      connected_node_ids.each do |node2_id|
        next if node1_id == node2_id #skip within-node connections
        sorted = [node1_id, node2_id].sort #sort so only a single connection is shown
        unless pairs_added.include?(sorted) or
          !nodes_to_explore.include?(graph.nodes[node1_id]) or
          !nodes_to_explore.include?(graph.nodes[node2_id]) or
          directly_connected_node_pairs.include?([node1_id, node2_id].sort)

          graphviz.add_edges sorted[0].to_s, sorted[1].to_s, {:color => "grey", :dir => "none", :style => 'dashed'}
          pairs_added << sorted
        end
      end
    end
  end

  return graphviz
end