Ten simple rules to create biological network figures for communication
Fig 3
Beware of unintended spatial interpretations.
This figure shows two illustrations representing the same region of the normalized structural mouse brain connectivity data set described by Ganglberger and colleagues [17]. The data are derived from the Allen Mouse Brain Connectome dataset [18]. The illustrations have been generated using the Cytoscape.js (Cytoscape Consortium; https://cytoscape.org/) implementation of the force-directed layout algorithm CoSE. The left image uses connectivity strength as the driving force for the layout, posing strongly connected nodes closely together, but at the same time neglecting the spatial context of the network. Instead, the second layout in the right image is driven by the spatial relation of brain regions, generating automatically a "flattened" mouse brain representation as seen from above. Symmetry and spatial positions are approximately reproduced. Structural connectivity strength is encoded by the gray-level color scale of the edges. CoSE, compound spring embedder.