Class "moduleWeb"

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Description

This class is the output of an application of the function computeModules(...) to a graph. It consists of the matrix representing the original graph which has been passed to computeModules(...) in order to compute modules, a matrix representing the same graph but permutated according to the identified modules, two vectors indicating the permutation of row and column indices, respectively, and information about the modules themselves.

Objects from the class

Objects from the class should only be created by using the function computeModules(...).

Slots

likelihood:

Contains a number with the likelihood-equivalent of the final proposed module structure. This value is the same value as Q (or M), the modularity as given by Newman or GuimerĂ  & Amaral (2005).

originalWeb:

Object of class "matrix" representing the original bipartite graph in which modules have been computed.

moduleWeb:

Object of class "matrix" representing the original bipartite graph but reordered such that plotting modules is possible.

orderA:

Object of class "vector" representing the permutation of the rows of the original graph.

orderB:

Object of class "vector" representing the permutation of the columns of the original graph.

modules:

Object of class "matrix" containing for each module the information about its depth and involved nodes.

Methods

Objects of this class are used in following functions:

listModuleInformation(moduleWebObject)

printoutModuleInformation(moduleWebObject)

plotModuleWeb(moduleWebObject, plotModules=TRUE, rank=FALSE, weighted=TRUE, displayAlabels=TRUE, displayBlabels=TRUE, labsize=1, plotsize=12, xlabel="", ylabel="", square.border="white", fromDepth=0, upToDepth=-1)

Author(s)

Rouven Strauss

Examples

1
showClass("moduleWeb")

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