Practical Matters: Working in Cytoscape:
See my Tutorial, An Introduction to Network Analysis and Cytoscape for XML Coders for a much more detailed explanation of how to read and make network graphs, and step-by-step advice on things you can do and try with Cytoscape’s network analyzer tools.
- (Write XSLT to output this from your XML: Here’s my XSLT to extract place tagging info from my XML to generate the .tsv import text
Use import wizard to designate nodes and edges, and node + edge attributes for use in labelling info.
Eliminate self-loops and remove duplicated edges in Edit menu (or find ways to filter out unnecessary information that clutters your graph).
Use the Network Analyzer to calculate network statistics. Think about them. Choose among graphical layouts with care.
Of interest in my original graph was Betweenness Centrality of Nodes. Where does my network of places break (cutpoints)? Metaplaces were essential to network coherence.
Now, I’ve generated some new graphs to simplify our view of the places, eliminate the clutter of line-group nodes (moving that information to the edges). And I’m interested in Path Lengths of Edges (Average Shortest Path Length), and Closeness of Nodes.
Here’s a new network graph oriented to Closeness Centrality of Nodes (SVG output from Cytoscape).
- I’ve remapped a network of place-to-place references only, and as before, without metaplaces, the network breaks.
- And when we view metaplace-to-metaplace references, this makes its own complete and coherent small-world network.
I’m also measuring the Eccentricity of the Nodes–how far they are from each other, which produced a rather remarkable result: (SVG output from Cytoscape)