Construct a bipartite graph — getBipartiteGraph • GeDi

Construct a bipartite graph from cluster information, mapping the cluster to its members

getBipartiteGraph(cluster, gs_names, genes)

Arguments

cluster: list, a list of clusters, cluster members are indicated by numeric values.
gs_names: vector, a vector of (geneset) identifiers/names to map the numeric member value in cluster to.
genes: list, a list of vectors of genenames which belong to the genesets in gs_names.

Value

An igraph object to be further manipulated or processed/plotted (e.g. via igraph::plot.igraph() or visNetwork::visIgraph())

Examples

cluster <- list(c(1:5), c(6:9))
gs_names <- c("a", "b", "c", "d", "e", "f", "g", "h", "i")
genes <- list(
  c("PDHB", "VARS2"), c("IARS2", "PDHA1"),
  c("AAAS", "ABCE1"), c("ABI1", "AAR2"), c("AATF", "AMFR"),
  c("BMS1", "DAP3"), c("AURKAIP1", "CHCHD1"), c("IARS2"),
  c("AHI1", "ALMS1")
)

g <- getBipartiteGraph(cluster, gs_names, genes)