Turn pairs or paths into a graph

Pairs are processed to produce a graph with the elements of the pairs as vertices and the pairs as undirected edges. The result can be displayed using plot() if the Bioconductor packages graph (for the graphNEL object) and optionally Rgraphviz (for plotting) are installed.

Usage

graph_pairs(x, var.names = NULL, edgemode = c("undirected", "directed"))

Arguments

x

matrix or list of pairs along a zenpath. Can also be a list containing vectors representing paths in the graph. Every path must be of length at least 2 (i.e. each vector element of the list).

var.names

names of the variables appearing in x.

edgemode

type of edges to be used: either "undirected" (the default) or "directed" (in which case the order of the nodes in each pair matters).

Value

a graphNEL object; can be displayed using plot() if Rgraphviz is installed.

Note

This function requires the Bioconductor package graph. If graph is not installed, an informative error is raised. Plotting also requires Rgraphviz, but all functionality of graph_pairs() is available without it.

See also

zenplot() which provides the zenplot.

Other tools related to constructing zenpaths: connect_pairs(), extract_pairs(), groupData(), indexData(), zenpath()

Author

Marius Hofert and Wayne Oldford

Examples

has_Rgraphviz <- requireNamespace("Rgraphviz", quietly = TRUE)
pairs <- matrix(c(1,2, 5,1, 3,4, 2,3, 4,2), ncol = 2, byrow = TRUE)
g <- graph_pairs(pairs)
if (has_Rgraphviz){
  Rgraphviz::plot(g)
}