igraph v1.1.2

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Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Functions in igraph

 Name Description adjacent_vertices Adjacent vertices of multiple vertices in a graph all_simple_paths List all simple paths from one source alpha_centrality Find Bonacich alpha centrality scores of network positions are_adjacent Are two vertices adjacent? E Edges of a graph V Vertices of a graph igraph-package The igraph package add_edges Add edges to a graph add_layout_ Add layout to graph add_vertices Add vertices to a graph as_adj_list Adjacency lists as_adjacency_matrix Convert a graph to an adjacency matrix assortativity Assortativity coefficient arpack_defaults ARPACK eigenvector calculation articulation_points Articulation points of a graph bipartite_mapping Decide whether a graph is bipartite bipartite_projection Project a bipartite graph canonical_permutation Canonical permutation of a graph categorical_pal Palette for categories centralize Centralization of a graph cliques The functions find cliques, ie. complete subgraphs in a graph as_ids Convert a vertex or edge sequence to an ordinary vector as_incidence_matrix Incidence matrix of a bipartite graph automorphisms Number of automorphisms cluster_louvain Finding community structure by multi-level optimization of modularity cluster_optimal Optimal community structure component_distribution Connected components of a graph compose Compose two graphs as binary relations as.directed Convert between directed and undirected graphs as.igraph Conversion to igraph biconnected_components Biconnected components centr_degree Centralize a graph according to the degrees of vertices centr_degree_tmax Theoretical maximum for degree centralization closeness Closeness centrality of vertices cluster_edge_betweenness Community structure detection based on edge betweenness bfs Breadth-first search estimate_betweenness Vertex and edge betweenness centrality c.igraph.es Concatenate edge sequences c.igraph.vs Concatenate vertex sequences cluster_label_prop Finding communities based on propagating labels authority_score Kleinberg's authority centrality scores. centr_betw Centralize a graph according to the betweenness of vertices centr_betw_tmax Theoretical maximum for betweenness centralization cluster_fast_greedy Community structure via greedy optimization of modularity cluster_spinglass Finding communities in graphs based on statistical meachanics cluster_walktrap Community strucure via short random walks consensus_tree Create a consensus tree from several hierarchical random graph models console The igraph console delete_vertex_attr Delete a vertex attribute delete_vertices Delete vertices from a graph distance_table Shortest (directed or undirected) paths between vertices diverging_pal Diverging palette cluster_infomap Infomap community finding complementer Complementer of a graph component_wise Component-wise layout count_isomorphisms Count the number of isomorphic mappings between two graphs curve_multiple Optimal edge curvature when plotting graphs decompose Decompose a graph into components dim_select Dimensionality selection for singular values using profile likelihood. disjoint_union Disjoint union of graphs count_motifs Graph motifs delete_edges Delete edges from a graph delete_graph_attr Delete a graph attribute dfs Depth-first search diameter Diameter of a graph edge_attr<- Set one or more edge attributes edge_attr Query edge attributes of a graph edge_density Graph density ego_size Neighborhood of graph vertices getAICc Compute AIC based on a Poisson Approximation using the output from gclust girth Girth of a graph graph_from_adjacency_matrix Create graphs from adjacency matrices cluster_leading_eigen Community structure detecting based on the leading eigenvector of the community matrix cocitation Cocitation coupling cohesive_blocks Calculate Cohesive Blocks constraint Burt's constraint graph_from_atlas Create a graph from the Graph Atlas hrg Create a hierarchical random graph from an igraph graph hrg_tree Create an igraph graph from a hierarchical random graph model hub_score Kleinberg's hub centrality scores. identical_graphs Decide if two graphs are identical igraph_options Parameters for the igraph package dyad_census Dyad census of a graph each_edge Rewires the endpoints of the edges of a graph to a random vertex embed_laplacian_matrix Spectral Embedding of the Laplacian of a Graph contract Contract several vertices into a single one degree Degree and degree distribution of the vertices delete_edge_attr Delete an edge attribute ends Incident vertices of some graph edges graph_attr<- Set all or some graph attributes graph_attr Graph attributes of a graph graph_from_lcf Creating a graph from LCF notation igraph_test Run package tests is_graphical Is a degree sequence graphical? is_igraph Is this object an igraph graph? is_weighted Weighted graphs diversity Graph diversity dominator_tree Dominator tree eigen_centrality Find Eigenvector Centrality Scores of Network Positions embed_adjacency_matrix Spectral Embedding of Adjacency Matrices as_edgelist Convert a graph to an edge list as_graphnel Convert igraph graphs to graphNEL objects from the graph package as_long_data_frame Convert a graph to a long data frame as_membership Declare a numeric vector as a membership vector graph_from_literal Creating (small) graphs via a simple interface gsize The size of the graph (number of edges) head_of Head of the edge(s) in a graph igraph-es-indexing2 Select edges and show their metadata igraph-minus Delete vertices or edges from a graph igraph_version Query igraph's version string incident Incident edges of a vertex in a graph intersection.igraph.es Intersection of edge sequences intersection.igraph.vs Intersection of vertex sequences centr_clo Centralize a graph according to the closeness of vertices centr_clo_tmax Theoretical maximum for closeness centralization centr_eigen Centralize a graph according to the eigenvector centrality of vertices centr_eigen_tmax Theoretical maximum for betweenness centralization membership Functions to deal with the result of network community detection compare Compares community structures using various metrics convex_hull Convex hull of a set of vertices coreness K-core decomposition of graphs difference.igraph.es Difference of edge sequences difference.igraph.vs Difference of vertex sequences edge_attr_names List names of edge attributes count_subgraph_isomorphisms Count the isomorphic mappings between a graph and the subgraphs of another graph count_triangles Find triangles in graphs difference Difference of two sets difference.igraph Difference of graphs isomorphic Decide if two graphs are isomorphic layout.reingold.tilford Deprecated layout functions layout_with_gem The GEM layout algorithm isomorphism_class Isomorphism class of a graph isomorphisms Calculate all isomorphic mappings between the vertices of two graphs layout_ Graph layouts graph_attr_names List names of graph attributes graph_from_adj_list Create graphs from adjacency lists as_data_frame Creating igraph graphs from data frames or vice-versa graph_from_edgelist Create a graph from an edge list matrix graph_id Get the id of a graph layout.fruchterman.reingold.grid Grid Fruchterman-Reingold layout, this was removed from igraph layout_as_bipartite Simple two-row layout for bipartite graphs layout_on_grid Simple grid layout layout_on_sphere Graph layout with vertices on the surface of a sphere layout_with_mds Graph layout by multidimensional scaling graph_version Igraph data structure versions igraph-vs-attributes Query or set attributes of the vertices in a vertex sequence igraph-vs-indexing Indexing vertex sequences igraph-vs-indexing2 Select vertices and show their metadata igraph_demo Run igraph demos, step by step is_chordal Chordality of a graph is_dag Directed acyclic graphs ivs Independent vertex sets keeping_degseq Graph rewiring while preserving the degree distribution layout_in_circle Graph layout with vertices on a circle. layout_nicely Choose an appropriate graph layout algorithm automatically layout_with_kk The Kamada-Kawai layout algorithm layout_with_graphopt The graphopt layout algorithm make_clusters Creates a communities object. make_de_bruijn_graph De Bruijn graphs make_tree Create tree graphs match_vertices Match Graphs given a seeding of vertex correspondences motifs Graph motifs mst Minimum spanning tree Drawing graphs Drawing graphs layout_with_sugiyama The Sugiyama graph layout generator make_lattice Create a lattice graph make_line_graph Line graph of a graph min_st_separators Minimum size vertex separators modularity.igraph Modularity of a community structure of a graph permute Permute the vertices of a graph %>% Magrittr's pipes power_centrality Find Bonacich Power Centrality Scores of Network Positions layout_with_lgl Large Graph Layout is_bipartite Create a bipartite graph make_chordal_ring Create an extended chordal ring graph make_ring Create a ring graph edge_connectivity Edge connectivity. fit_power_law Fitting a power-law distribution function to discrete data gclust.app Graph Clustering Using NMF (and no SVT) -- Apparent Clusters plot.igraph Plotting of graphs plot_dendrogram.igraphHRG HRG dendrogram plot +.igraph Add vertices, edges or another graph to a graph gclust.rsvt Graph Clustering Using SVT and NMF -- Clusters Implied by Singular Value Thresholding get.edge.ids Find the edge ids based on the incident vertices of the edges graph_from_graphdb Load a graph from the graph database for testing graph isomorphism. predict_edges Predict edges based on a hierarchical random graph model rep.igraph Replicate a graph multiple times rev.igraph.es Reverse the order in an edge sequence sample_correlated_gnp Generate a new random graph from a given graph by randomly adding/removing edges sample_correlated_gnp_pair Sample a pair of correlated G(n,p) random graphs graph_from_graphnel Convert graphNEL objects from the graph package to igraph head_print Print the only the head of an R object hrg-methods Hierarchical random graphs sample_dot_product Generate random graphs according to the random dot product graph model sample_fitness Random graphs from vertex fitness scores sample_pref Trait-based random generation sample_sbm Sample stochastic block model eccentricity Eccentricity of the vertices in a graph edge Helper function for adding and deleting edges erdos.renyi.game Generate random graphs according to the Erdos-Renyi model fit_hrg Fit a hierarchical random graph model scg_semi_proj Semi-Projectors sequential_pal Sequential palette simplify Simple graphs time_bins.sir SIR model on graphs make_star Create a star graph, a tree with n vertices and n - 1 leaves min_cut Minimum cut in a graph min_separators Minimum size vertex separators norm_coords Normalize coordinates for plotting graphs gorder Order (number of vertices) of a graph graph_ Convert object to a graph graph_from_incidence_matrix Create graphs from an incidence matrix graph_from_isomorphism_class Create a graph from an isomorphism class graphlet_basis Graphlet decomposition of a graph groups Groups of a vertex partitioning igraph-es-attributes Query or set attributes of the edges in an edge sequence igraph-es-indexing Indexing edge sequences igraph-attribute-combination How igraph functions handle attributes when the graph changes igraph-dollar Getting and setting graph attributes, shortcut incident_edges Incident edges of multiple vertices in a graph indent_print Indent a printout is_degseq Check if a degree sequence is valid for a multi-graph is_directed Check whether a graph is directed is_printer_callback Is this a printer callback? is_separator Vertex separators st_min_cuts List all minimum $(s,t)$-cuts of a graph stochastic_matrix Stochastic matrix of a graph transitivity Transitivity of a graph intersection Intersection of two or more sets intersection.igraph Intersection of graphs is_named Named graphs knn Average nearest neighbor degree laplacian_matrix Graph Laplacian layout.spring Spring layout, this was removed from igraph layout.svd SVD layout, this was removed from igraph layout_as_star Generate coordinates to place the vertices of a graph in a star-shape layout_as_tree The Reingold-Tilford graph layout algorithm layout_randomly Randomly place vertices on a plane or in 3d space layout_with_dh The Davidson-Harel layout algorithm is_min_separator Minumal vertex separators layout_with_drl The DrL graph layout generator layout_with_fr The Fruchterman-Reingold layout algorithm make_empty_graph A graph with no edges make_full_bipartite_graph Create a full bipartite graph radius Radius of a graph random_walk Random walk on a graph rev.igraph.vs Reverse the order in a vertex sequence rewire Rewiring edges of a graph make_graph Create an igraph graph from a list of edges, or a notable graph make_kautz_graph Kautz graphs is_matching Graph matching max_cardinality Maximum cardinality search sample_gnm Generate random graphs according to the G(n,m) Erdos-Renyi model sample_gnp Generate random graphs according to the G(n,p) Erdos-Renyi model sample_pa Generate scale-free graphs according to the Barabasi-Albert model sample_pa_age Generate an evolving random graph with preferential attachment and aging sample_sphere_surface Sample vectors uniformly from the surface of a sphere sample_sphere_volume Sample vectors uniformly from the volume of a sphere set_edge_attr Set edge attributes normalize Normalize layout plot.sir Plotting the results on multiple SIR model runs plot_dendrogram Community structure dendrogram plots read_graph Reading foreign file formats set_graph_attr Set a graph attribute subgraph Subgraph of a graph subgraph_centrality Find subgraph centrality scores of network positions unfold_tree Convert a general graph into a forest triad_census Triad census, subgraphs with three vertices union.igraph Union of graphs union.igraph.es Union of edge sequences without_attr Construtor modifier to remove all attributes from a graph without_loops Constructor modifier to drop loop edges reciprocity Reciprocity of graphs sample_ Sample from a random graph model sample_bipartite Bipartite random graphs sample_fitness_pl Scale-free random graphs, from vertex fitness scores sample_forestfire Forest Fire Network Model union Union of two or more sets vertex_attr<- Set one or more vertex attributes vertex_attr Query vertex attributes of a graph with_edge_ Constructor modifier to add edge attributes sample_seq Sampling a random integer sequence sample_smallworld The Watts-Strogatz small-world model scg_eps Error of the spectral coarse graining (SCG) approximation scg_group SCG Problem Solver page_rank The Page Rank algorithm path Helper function to add or delete edges along a path print.igraph.vs Show a vertex sequence on the screen print.igraphHRG Print a hierarchical random graph model to the screen printr Better printing of R packages r_pal The default R palette sample_degseq Generate random graphs with a given degree sequence sample_dirichlet Sample from a Dirichlet distribution sample_hierarchical_sbm Sample the hierarchical stochastic block model with_graph_ Constructor modifier to add graph attributes set_vertex_attr Set vertex attributes shapes Various vertex shapes when plotting igraph graphs strength Strength or weighted vertex degree [.igraph Query and manipulate a graph as it were an adjacency matrix local_scan Compute local scan statistics on graphs make_ Make a new graph make_full_citation_graph Create a complete (full) citation graph make_full_graph Create a full graph max_flow Maximum flow in a graph sample_hrg Sample from a hierarchical random graph model sample_last_cit Random citation graphs sample_motifs Graph motifs sample_traits_callaway Graph generation based on different vertex types neighbors Neighboring (adjacent) vertices in a graph print.nexusDatasetInfo Query and download from the Nexus network repository print.igraph Print graphs to the terminal print.igraph.es Print an edge sequence to the screen tkplot Interactive plotting of graphs topo_sort Topological sorting of vertices in a graph unique.igraph.vs Remove duplicate vertices from a vertex sequence upgrade_graph Igraph data structure versions merge_coords Merging graph layouts print.igraphHRGConsensus Print a hierarchical random graph consensus tree to the screen printer_callback Create a printer callback function rglplot 3D plotting of graphs with OpenGL which_multiple Find the multiple or loop edges in a graph which_mutual Find mutual edges in a directed graph running_mean Running mean of a time series sample_grg Geometric random graphs sample_growing Growing random graph generation sample_islands A graph with subgraphs that are each a random graph. sample_k_regular Create a random regular graph scg-method Spectral Coarse Graining scg All-in-one Function for the SCG of Matrices and Graphs spectrum Eigenvalues and eigenvectors of the adjacency matrix of a graph scan_stat Scan statistics on a time series of graphs similarity Similarity measures of two vertices simplified Constructor modifier to drop multiple and loop edges split_join_distance Split-join distance of two community structures srand Deprecated function, used to set random seed of the C library's RNG st_cuts List all (s,t)-cuts of a graph tail_of Tails of the edge(s) in a graph tkigraph Experimental basic igraph GUI vertex Helper function for adding and deleting vertices Pie charts as vertices Using pie charts as vertices in graph plots with_igraph_opt Run code with a temporary igraph options setting [[.igraph Query and manipulate a graph as it were an adjacency list subcomponent In- or out- component of a vertex subgraph_isomorphic Decide if a graph is subgraph isomorphic to another one subgraph_isomorphisms All isomorphic mappings between a graph and subgraphs of another graph union.igraph.vs Union of vertex sequences unique.igraph.es Remove duplicate edges from an edge sequence vertex_attr_names List names of vertex attributes vertex_connectivity Vertex connectivity. without_multiples Constructor modifier to drop multiple edges write_graph Writing the graph to a file in some format with_vertex_ Constructor modifier to add vertex attributes No Results!