overlap (modules, algorithm = c("mds", "fr", "drl"), edge.limit = 0.5)
overlapPlot (graph, xsize = 400, ysize = 400, vertex.size = 20, vertex.size2 = 10, ...)ISAModules object.edge.limit will be drawn.igraph object, as returned by overlap.plot.igraph function from the igraph package.overlap returns an igraph graph.overlapPlot returns the coordinates of the vertices in a
two-column matrix, invisibly.
ISAModules object may potentially contain many
modules that overlap. These functions visualize the overlapping
relationships of a set of modules. overlap creates an igraph graph with additional
information on how to plot this graph in a way that nodes representing
overlapping modules are close to each other.
overlapPlot takes such a graph and plots it.
overlap can use various algorithms, depending on the
algorithm argument. If it is ‘mds’, then
multi-dimensional scaling is used, by calling the
isaMDS function in the MASS package.
If it is ‘fr’, then
the Fruchterman-Reingold algorithm is used, through the
layout.fruchterman.reingold function of the igraph
package. If it is ‘drl’, then the DrL graph layout
algorithm is used, see the layout.drl function
in the igraph0 package.
data(ALLModulesSmall)
G <- overlap(ALLModulesSmall, algorithm="drl", edge.limit=0.3)
if (interactive()) {
overlapPlot(G)
}
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