Write a graph matrix to a GraphML file

Writes an undirected weighted graph to a .graphml file with igraph::write_graph(), for use in external tools such as Gephi.

Usage

precise_graphml(data, file, key = NULL)

Arguments

data: A square symmetric numeric matrix, or a tibble from which key= selects one similarity-typed row.
file: Path of the .graphml file to write.
key: When data is a tibble, the distance or method value of the row to export. It is required for tibble input and must match exactly one row.

Value

Invisibly, the normalized path that was written.

Details

data is either a bare square symmetric numeric matrix or a tibble from which key= selects exactly one row. Matrix input may come from any producer.

Input must be square, symmetric within 1e-8, and finite. A tibble row must be typed similarity; other declared types are outside the export contract. In particular, distance values would invert the meaning of edge weight. A bare matrix carries no declared type and is written as supplied. The diagonal is excluded from the exported edges.

An existing file is an error. Nothing is overwritten.

References

Csardi G, Nepusz T (2006). The igraph software package for complex network research. InterJournal Complex Systems, 1695.

Author

Brian Muchmore

Examples

data(data_cell_cycle, package = "PreciseViz")

cells <- c(1:4, 60:63, 118:121)
cell_cycle <- as.matrix(data_cell_cycle[cells, 2:41])
rownames(cell_cycle) <- paste0(data_cell_cycle$Cell_cycle[cells], "_", cells)

euclidean <- as.matrix(stats::dist(cell_cycle))
adjacency <- (euclidean <= stats::quantile(euclidean[lower.tri(euclidean)],
                                           0.25)) * 1
diag(adjacency) <- 0

graphml_file <- tempfile(fileext = ".graphml")
precise_graphml(adjacency, graphml_file)
file.exists(graphml_file)
#> [1] TRUE