make_adjmatrix {graphsim}

Generate Adjacency Matrix

Description

Compute the adjacency matrix of a (directed) igraph structure, preserving node/column/row names (and direction).

Usage

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.

Value

An adjacency matrix compatible with generating an expression matrix

Author(s)

Tom Kelly [e-mail]

See Also

See also generate_expression for computing the simulated data, make_sigma for computing the Sigma (\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

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]