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Create graphs from a bipartite adjacency matrix

Source: R/incidence.R
graph_from_biadjacency_matrix.Rd

graph_from_biadjacency_matrix() creates a bipartite igraph graph from an incidence matrix.

Usage

graph_from_biadjacency_matrix(
  incidence,
  directed = FALSE,
  mode = c("all", "out", "in", "total"),
  multiple = FALSE,
  weighted = NULL,
  add.names = NULL
)

Arguments

incidence

The input bipartite adjacency matrix. It can also be a sparse matrix from the Matrix package.

directed

Logical scalar, whether to create a directed graph.

mode

A character constant, defines the direction of the edges in directed graphs, ignored for undirected graphs. If ‘out’, then edges go from vertices of the first kind (corresponding to rows in the bipartite adjacency matrix) to vertices of the second kind (columns in the incidence matrix). If ‘in’, then the opposite direction is used. If ‘all’ or ‘total’, then mutual edges are created.

multiple

Logical scalar, specifies how to interpret the matrix elements. See details below.

weighted

This argument specifies whether to create a weighted graph from the bipartite adjacency matrix. If it is NULL then an unweighted graph is created and the multiple argument is used to determine the edges of the graph. If it is a character constant then for every non-zero matrix entry an edge is created and the value of the entry is added as an edge attribute named by the weighted argument. If it is TRUE then a weighted graph is created and the name of the edge attribute will be ‘weight’.

add.names

A character constant, NA or NULL. graph_from_biadjacency_matrix() can add the row and column names of the incidence matrix as vertex attributes. If this argument is NULL (the default) and the bipartite adjacency matrix has both row and column names, then these are added as the ‘name’ vertex attribute. If you want a different vertex attribute for this, then give the name of the attributes as a character string. If this argument is NA, then no vertex attributes (other than type) will be added.

Value

A bipartite igraph graph. In other words, an igraph graph that has a vertex attribute type.

Details

Bipartite graphs have a ‘type’ vertex attribute in igraph, this is boolean and FALSE for the vertices of the first kind and TRUE for vertices of the second kind.

graph_from_biadjacency_matrix() can operate in two modes, depending on the multiple argument. If it is FALSE then a single edge is created for every non-zero element in the bipartite adjacency matrix. If multiple is TRUE, then the matrix elements are rounded up to the closest non-negative integer to get the number of edges to create between a pair of vertices.

Some authors refer to the bipartite adjacency matrix as the "bipartite incidence matrix". igraph 1.6.0 and later does not use this naming to avoid confusion with the edge-vertex incidence matrix.

See also

make_bipartite_graph() for another way to create bipartite graphs

Other biadjacency: as_data_frame()

Author

Gabor Csardi csardi.gabor@gmail.com

Examples


inc <- matrix(sample(0:1, 15, repl = TRUE), 3, 5)
colnames(inc) <- letters[1:5]
rownames(inc) <- LETTERS[1:3]
graph_from_biadjacency_matrix(inc)
#> IGRAPH 9fbebc3 UN-B 8 9 -- 
#> + attr: type (v/l), name (v/c)
#> + edges from 9fbebc3 (vertex names):
#> [1] A--c A--d A--e B--a B--d B--e C--b C--c C--e