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Team-based Cytoscape Exercise
Today’s class is a joint meeting with the Introduction to DH class and Prof. Jacob’s Paper Trails in Victorian Literature class. We will have some discussion under our belts about DH, about visualization, and about how we can and cannot learn about literature – in this case Wharton’s House of Mirth – through visualizations with Cytoscape.
Objective
The assignment today will be akin to a lab in which you might have participated as part of, say, your chemistry or biology course. (Please don’t tell your chemistry or biology profs: ours is much less scientific, but there is method.)
In teams of four – and your teams should have at least two members from each class – you’ll work on (A) designing visualizations that answer a few questions and (B), using the methods involved with creating visualizations in Cytoscape, formulate questions of your own might be answerable through the visualization of textual data.
The Questions
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Regarding “Nature of Exchange,” which kinds of exchange are at the center of the novel? Which are at the periphery? Who’s involved in the most central kinds of exchange? Who’s involved in the most peripheral?
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Who is sending what kind of messages? For the third variable, you might add (as the edge/interaction): to whom are they sending them? what is the nature of that exchange? how is the message delivered?
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Broadly speaking, what kinds of exchanges are predominantly in person? What kinds of exchanges are exclusively in person?
ProTips
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The input screen when you’re uploading to Cytoscape is a menu of tripartite options: choose a source node, a target node, and an edge (or interaction type) for each trial you want to run. Like our questions above, try to formulate a sentence that helps frame the question you’d like to visualize.
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My favorite (and to my mind some of the most useful) settings include:
- Style: Curved, with Edges labeled (Passthrough Mapping), and sometimes with the edges separated out (Layout>Clear All Edge Bends)
- Layout: Interactive, with No Acceleration, using the “Edge Repulsive Fruchterman-Reingold” algorithm. (Remember to “Run” when you’re ready, and to tinker with the “Scale”.)
Downloads
- Cytoscape, if you want it.
- AllegroLayout is a set of algorithms that allow us to create more dynamic network visualizations.
- The House of Mirth dataset from our class Moodle (Paper Trails folks might have their own access.)
Helpful (?) links
About Force Directed Layouts
Color Scheme Generator
An Introduction to Digital Humanities by Jacob Heil is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.