condorMatrixModularity: Iteratively maximize bipartite modularity.

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Iteratively maximize bipartite modularity.

Description

This function is based on the bipartite modularity as defined in "Modularity and community detection in bipartite networks" by Michael J. Barber, Phys. Rev. E 76, 066102 (2007) This function uses a slightly different implementation from the paper. It does not use the "adaptive BRIM" method for identifying the number of modules. Rather, it simply continues to iterate until the difference in modularity between iterations is less that 10^-4. Starting from a random initial condition, this could take some time. Use condorCluster for quicker runtimes and likely better clustering, it initializes the blue node memberships by projecting the blue nodes into a unipartite "blue" network and then identify communities in that network using a standard unipartite community detection algorithm run on the projected network. See condorCluster for more details on that. This function loads the entire adjacency matrix in memory, so if your network has more than ~50,000 nodes, you may want to use condorModularityMax, which is slower, but does not store the matrices in memory. Or, of course, you could move to a larger machine.

Usage

condorMatrixModularity(
  condor.object,
  T0 = cbind(seq_len(q), rep(1, q)),
  weights = 1,
  deltaQmin = "default"
)

Arguments

condor.object	is a list created by createCondorObject. condor.object$edges must contain the edges in the giant connected component of a bipartite network
T0	is a two column data.frame with the initial community assignment for each "blue" node, assuming there are more reds than blues, though this is not strictly necessary. The first column contains the node name, the second column the community assignment.
weights	edgeweights for each edge in edgelist.
deltaQmin	convergence parameter determining the minimum required increase in the modularity for each iteration. Default is min(10^-4,1/(number of edges)), with number of edges determined by nrow(condor.object$edges). User can set this parameter by passing a numeric value to deltaQmin.

Value

Qcoms data.frame with modularity of each community.

modularity modularity value after each iteration.

red.memb community membership of the red nodes

blue.memb community membership of the blue.nodes

Examples

r = c(1,1,1,2,2,2,3,3,3,4,4);
b = c(1,2,3,1,2,4,2,3,4,3,4);
reds <- c("Alice","Sue","Janine","Mary")
blues <- c("Bob","John","Ed","Hank")
elist <- data.frame(red=reds[r],blue=blues[b])
condor.object <- createCondorObject(elist)
#randomly assign blues to their own community
T0 <- data.frame(nodes=blues,coms=seq_len(4))
condor.object <- condorMatrixModularity(condor.object,T0=T0)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.