Advertisement

< Back to Article

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference

Figure 1

Community structure in graphs and affinity matrices.

(A) A graph with 10 vertices and 22 edges. Thick black lines denote strong edges and thin dotted lines denote weak edges. The edge classes have been drawn so that the distinction between them is prominent: {1,2,3,4} and {5,6,7,8,9,10} are intuitive communities of connected vertices. (B) Ostensibly the same graph as in the previous panel, with the edge classes drawn to obscure the communities that were so prominent. (C) Depiction of the affinity matrix that corresponds to the graph in panel (A). Rows and columns denote vertices, and each (row,column) entry of the matrix is shaded to indicate the strength of its corresponding edge, if any. As drawn, the contrast between strong and weak edges is sufficient to reveal two communities as clusters of darkly shaded squares along the matrix main diagonal. (D) Depiction of the affinity matrix that corresponds to the graph in panel (B). With less contrast between edge classes, the pattern along the main diagonal is largely obscured.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1000479.g001