make_adjmatrix function

Generate Adjacency Matrix

Generate Adjacency Matrix

Compute the adjacency matrix of a (directed) igraph

structure, preserving node/column/row names (and direction).

make_adjmatrix_graph(graph, directed = FALSE)

Arguments

  • graph: An igraph object. May be directed or weighted.
  • directed: logical. Whether directed information is passed to the adjacency matrix.

Returns

An adjacency matrix compatible with generating an expression matrix

Examples

# construct a synthetic graph module library("igraph") graph_test_edges <- rbind(c("A", "B"), c("B", "C"), c("B", "D")) graph_test <- graph.edgelist(graph_test_edges, directed = TRUE) # compute adjacency matrix for toy example adjacency_matrix <- make_adjmatrix_graph(graph_test) adjacency_matrix # construct a synthetic graph network graph_structure_edges <- rbind(c("A", "C"), c("B", "C"), c("C", "D"), c("D", "E"), c("D", "F"), c("F", "G"), c("F", "I"), c("H", "I")) graph_structure <- graph.edgelist(graph_structure_edges, directed = TRUE) # compute adjacency matrix for toy network graph_structure_adjacency_matrix <- make_adjmatrix_graph(graph_structure) graph_structure_adjacency_matrix # import graph from package for reactome pathway # TGF-\eqn{\Beta} receptor signaling activates SMADs (R-HSA-2173789) TGFBeta_Smad_graph <- identity(TGFBeta_Smad_graph) # compute adjacency matrix for TGF-\eqn{\Beta} receptor signaling activates SMADs TGFBeta_Smad_adjacency_matrix <- make_adjmatrix_graph(TGFBeta_Smad_graph) dim(TGFBeta_Smad_adjacency_matrix) TGFBeta_Smad_adjacency_matrix[1:12, 1:12]

See Also

See also generate_expression for computing the simulated data, make_sigma for computing the Sigma (Σ\Sigma) matrix, make_distance for computing distance from a graph object, make_state for resolving inhibiting states.

See also plot_directed for plotting graphs or heatmap.2 for plotting matrices.

See also make_laplacian

or make_commonlink for computing input matrices.

See also igraph for handling graph objects.

Other graphsim functions: generate_expression(), make_commonlink, make_distance, make_laplacian, make_sigma, make_state, plot_directed()

Other graph conversion functions: make_commonlink, make_laplacian

Author(s)

Tom Kelly tom.kelly@riken.jp