Fig. 3: Diverse patterns emerge in the co-abundance networks of bacterial species across cities. | Nature Communications

Fig. 3: Diverse patterns emerge in the co-abundance networks of bacterial species across cities.

From: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

Fig. 3

a Each vertex corresponds to a species’ genome, and the links represent significant positive (blue) and negative (red) correlations. The size of the vertices is proportional to the mean CLR-transformed depth of coverage, and the shapes encode variance level. Vertex colors are used to highlight the community membership. For the vertex placement, we used the Fruchterman-Reingold layout algorithm on the subgraph composed from only positive edges. Following this representation, many of the blue/positive links are covered by the circles, even if there are more positive links overall, see Supplementary Table S1). b Heatmap of the Jaccard similarity (J) with the hierarchical clustering of the Jaccard dissimilarity (1-J). The index J is defined as the ratio of the intersection of the links shared between two networks with respect to the union. See Supplementary Fig. S4 for an analogous version with nodes colored by taxonomy.

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