bloody noob in Cytoscape here and my Google skills have abandoned me.
I am working on a university project to implement a simplefied pipeline to use data from NCBI GEO to reconstruct networks found in this paper.
A running version of the pipeline exists and I am able to generate a nice source-interaction-target-score table to load in Cytoscape. Now here is my problem. One Cytoscape example session for the aforementioned paper looks like this:
In contrast, using the default "Prefuse Force Directed Layout" when importing my own generated network file will yield something like this:
My question is mostly: what is the reason for this and how can I fix it? The tables which are fed into Cytoscape are similar, although node number, edge number, and scores (edge weights) do vary. If I apply the default layout on the correct example layout, it will look like my own network. Is there a setting I need to change? A plugin to use?