Class: IGraph

Inherits:
Object
  • Object
show all
Includes:
Enumerable, Cliques, Closeness, Community, Components, Connectivity, FileRead, FileWrite, Generate, GenerateRandom, IndependentVertexSets, Isomorphism, KCores, Layout, MinimumCuts, Motifs, Neighborhood, OtherOperations, Randomise, ShortestPaths, Sorting, Spanning, Spectral, Transitivity
Defined in:
ext/cIGraph.c

Defined Under Namespace

Modules: Cliques, Closeness, Community, Components, Connectivity, FileRead, FileWrite, Generate, GenerateRandom, IndependentVertexSets, Isomorphism, KCores, Layout, MinimumCuts, Motifs, Neighborhood, OtherOperations, Randomise, ShortestPaths, Sorting, Spanning, Spectral, Transitivity

Constant Summary collapse

VERSION =

in cIGraph_community.c

rb_str_new2("0.9.1")
EDGEORDER_ID = 
INT2NUM(1)
EDGEORDER_FROM = 
INT2NUM(2)
EDGEORDER_TO = 
INT2NUM(3)
OUT = 
INT2NUM(1)
IN = 
INT2NUM(2)
ALL = 
INT2NUM(3)
TOTAL = 
INT2NUM(4)
ARBITRARY = 
INT2NUM(0)
MUTUAL = 
INT2NUM(1)
EACH = 
INT2NUM(0)
COLLAPSE = 
INT2NUM(1)
ERDOS_RENYI_GNP = 
INT2NUM(0)
ERDOS_RENYI_GNM = 
INT2NUM(1)

Constants included from Generate

Generate::ADJ_DIRECTED, Generate::ADJ_LOWER, Generate::ADJ_MAX, Generate::ADJ_MIN, Generate::ADJ_PLUS, Generate::ADJ_UNDIRECTED, Generate::ADJ_UPPER, Generate::STAR_IN, Generate::STAR_OUT, Generate::STAR_UNDIRECTED, Generate::TREE_IN, Generate::TREE_OUT, Generate::TREE_UNDIRECTED

Constants included from Components

Components::STRONG, Components::WEAK

Constants included from OtherOperations

OtherOperations::GET_ADJACENCY_BOTH, OtherOperations::GET_ADJACENCY_LOWER, OtherOperations::GET_ADJACENCY_UPPER

Constants included from Connectivity

Connectivity::VCONN_NEI_ERROR, Connectivity::VCONN_NEI_IGNORE, Connectivity::VCONN_NEI_INFINITY

Constants included from Community

Community::SPINCOMM_UPDATE_CONFIG, Community::SPINCOMM_UPDATE_SIMPLE

Instance Method Summary collapse

Methods included from Generate

adjacency, atlas, extended_chordal_ring, full, isoclass_create, lattice, ring, star, tree

Methods included from GenerateRandom

asymmetric_preference_game, barabasi_aging_game, barabasi_game, callaway_traits_game, cited_type_game, citing_cited_type_game, degree_sequence_game, erdos_renyi_game, establishment_game, grg_game, growing_random_game, nonlinear_barabasi_game, preference_game, recent_degree_aging_game, recent_degree_game, watts_strogatz_game

Methods included from Randomise

#rewire, #rewire_edges

Methods included from ShortestPaths

#average_path_length, #diameter, #dijkstra_shortest_paths, #get_all_shortest_paths, #get_shortest_paths, #girth, #shortest_paths

Methods included from Neighborhood

#connect_neighborhood, #neighbourhood, #neighbourhood_graphs, #neighbourhood_size

Methods included from Components

#clusters, #decompose, #subcomponent, #subgraph

Methods included from Closeness

#betweenness, #closeness, #constraint, #edge_betweenness, #maxdegree, #pagerank

Methods included from Spanning

#minimum_spanning_tree_prim, #minimum_spanning_tree_unweighted

Methods included from Transitivity

#transitivity, #transitivity_avglocal, #transitivity_local

Methods included from Spectral

#laplacian

Methods included from KCores

#coreness

Methods included from OtherOperations

#bibcoupling, #cocitation, #density, #get_adjacency, #reciprocity, #simplify

Methods included from Cliques

#clique_number, #cliques, #largest_cliques, #maximal_cliques

Methods included from IndependentVertexSets

#independence_number, #independent_vertex_sets, #largest_independent_vertex_sets, #maximal_independent_vertex_sets

Methods included from Isomorphism

#isoclass, #isoclass_subgraph, #isomorphic, #isomorphic_vf2

Methods included from Motifs

#motifs_randesu, #motifs_randesu_estimate, #motifs_randesu_no

Methods included from Sorting

#topological_sorting

Methods included from FileRead

read_graph_dimacs, read_graph_edgelist, read_graph_gml, read_graph_graphdb, read_graph_graphml, read_graph_lgl, read_graph_ncol, read_graph_pajek

Methods included from FileWrite

#write_graph_dimacs, #write_graph_edgelist, #write_graph_gml, #write_graph_graphml, #write_graph_lgl, #write_graph_ncol, #write_graph_pajek

Methods included from Layout

#layout_circle, #layout_fruchterman_reingold, #layout_fruchterman_reingold_3d, #layout_grid_fruchterman_reingold, #layout_kamada_kawai, #layout_kamada_kawai_3d, #layout_lgl, layout_merge_dla, #layout_random, #layout_random_3d, #layout_reingold_tilford, #layout_reingold_tilford_circular, #layout_sphere

Methods included from MinimumCuts

#maxflow_value, #mincut, #mincut_value, #st_mincut_value

Methods included from Connectivity

#adhesion, #cohesion, #edge_connectivity, #edge_disjoint_paths, #st_edge_connectivity, #st_vertex_connectivity, #vertex_connectivity, #vertex_disjoint_paths

Methods included from Community

#community_eb_get_merges, #community_edge_betweenness, #community_fastgreedy, #community_leading_eigenvector, #community_leading_eigenvector_naive, #community_leading_eigenvector_step, #community_spinglass, #community_spinglass_single, #community_to_membership, #community_walktrap, #modularity

Constructor Details

#new(edges, directed) ⇒ IGraph

Creates a new IGraph graph with the edges specified in the edges Array. The first two elements define the first edge (the order is from,to for directed graphs). The next two define the second edge and so on. The Array should contain an even number of elements. Graph elements can be any ruby object.

The boolean value directed specifies whether a directed or undirected graph is created.

Example:

IGraph.new([1,2,3,4],true)

Creates a graph with four vertices. Vertex 1 is connected to vertex 2. Vertex 3 is connected to vertex 4.



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# File 'ext/cIGraph.c', line 78

VALUE cIGraph_initialize(int argc, VALUE *argv, VALUE self){

  igraph_t *graph;
  igraph_vector_t edge_v;
  VALUE vertex;
  VALUE directed;
  VALUE edges;
  VALUE attrs;
  VALUE v_ary;
  int vertex_n = 0;
  int current_vertex_id;
  int i;

  igraph_vector_ptr_t vertex_attr;
  igraph_vector_ptr_t edge_attr;

  igraph_i_attribute_record_t v_attr_rec;
  v_attr_rec.name  = "__RUBY__";
  v_attr_rec.type  = IGRAPH_ATTRIBUTE_PY_OBJECT;
  v_attr_rec.value = (void*)rb_ary_new();

  igraph_i_attribute_record_t e_attr_rec;
  e_attr_rec.name  = "__RUBY__";
  e_attr_rec.type  = IGRAPH_ATTRIBUTE_PY_OBJECT;
  e_attr_rec.value = (void*)rb_ary_new();

  rb_scan_args(argc,argv,"12", &edges, &directed, &attrs);

  //Initialize edge vector
  IGRAPH_FINALLY(igraph_vector_destroy,&edge_v);
  IGRAPH_FINALLY(igraph_vector_ptr_destroy,&vertex_attr);
  IGRAPH_FINALLY(igraph_vector_ptr_destroy,&edge_attr);

  IGRAPH_CHECK(igraph_vector_init_int(&edge_v,0));

  IGRAPH_CHECK(igraph_vector_ptr_init(&vertex_attr,0));
  IGRAPH_CHECK(igraph_vector_ptr_init(&edge_attr,0));

  Data_Get_Struct(self, igraph_t, graph);

  v_ary = rb_ary_new();

  if(!directed)
    IGRAPH_CHECK(igraph_to_undirected(graph,IGRAPH_TO_UNDIRECTED_COLLAPSE));

  //Loop through objects in edge Array
  for (i=0; i<RARRAY_LEN(edges); i++) {
    vertex = RARRAY_PTR(edges)[i];
    if(rb_ary_includes(v_ary,vertex)){
      //If @vertices includes this vertex then look up the vertex number
      current_vertex_id = NUM2INT(rb_funcall(v_ary,rb_intern("index"),1,vertex));
    } else {
      //Otherwise add to the list of vertices
      rb_ary_push(v_ary,vertex);
      current_vertex_id = vertex_n;
      vertex_n++;
      
      //Add object to list of vertex attributes
      rb_ary_push((VALUE)v_attr_rec.value,vertex);
      
    }
    IGRAPH_CHECK(igraph_vector_push_back(&edge_v,current_vertex_id));
    if (i % 2){
      if (attrs != Qnil){
	rb_ary_push((VALUE)e_attr_rec.value,RARRAY_PTR(attrs)[i/2]);
      } else {
	rb_ary_push((VALUE)e_attr_rec.value,Qnil);
      }
    }
  }

  IGRAPH_CHECK(igraph_vector_ptr_push_back(&vertex_attr, &v_attr_rec));
  IGRAPH_CHECK(igraph_vector_ptr_push_back(&edge_attr,   &e_attr_rec));

  if(igraph_vector_size(&edge_v) > 0){
    IGRAPH_CHECK(igraph_add_vertices(graph,vertex_n,&vertex_attr));
    IGRAPH_CHECK(igraph_add_edges(graph,&edge_v,&edge_attr));
  }

  igraph_vector_destroy(&edge_v);
  igraph_vector_ptr_destroy(&vertex_attr);
  igraph_vector_ptr_destroy(&edge_attr);

  IGRAPH_FINALLY_CLEAN(3);

  return self;

}

Instance Method Details

#[] ⇒ Object Also known as: get_edge_attr

#[]= ⇒ Object Also known as: set_edge_attr

#add_edge ⇒ Object

#add_edges ⇒ Object

#add_vertex ⇒ Object

#add_vertices ⇒ Object

#adjacent ⇒ Object

#adjacent_edges ⇒ Object

#adjacent_vertices ⇒ Object

#are_connected ⇒ Object Also known as: are_connected?

#attributes ⇒ Object

#degree ⇒ Object

#delete_edge ⇒ Object

#delete_vertex ⇒ Object

#each_edge ⇒ Object

#each_edge_eid ⇒ Object

#each_vertex ⇒ Object Also known as: each

#ecount ⇒ Object

#edge ⇒ Object

#edges ⇒ Object Also known as: all_edges

#get_eid ⇒ Object

#initialize_copy(orig) ⇒ Object

Internal method for copying IGraph objects.



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# File 'ext/cIGraph.c', line 37

VALUE cIGraph_init_copy(VALUE copy, VALUE orig){

  igraph_t *orig_graph;
  igraph_t *copy_graph;

  if (copy == orig)
    return copy;

  if(TYPE(orig) != T_DATA || RDATA(orig)->dfree != (RUBY_DATA_FUNC)cIGraph_free){
    rb_raise(rb_eTypeError, "Wrong argument type.");
  }
  
  Data_Get_Struct(copy, igraph_t, copy_graph); 
  Data_Get_Struct(orig, igraph_t, orig_graph);

  IGRAPH_CHECK(igraph_copy(copy_graph,orig_graph));

  return copy;

}

#is_directed? ⇒ Boolean Also known as: is_directed

Returns:

  • (Boolean)

#neighbours ⇒ Object Also known as: neighbors

#nonadjacent_vertices ⇒ Object

#to_directed ⇒ Object

#to_undirected ⇒ Object

#vcount ⇒ Object

#vertices ⇒ Object Also known as: all_vertices