We upgraded Copycat to enable Cytoscape Automationĥ, thereby bringing the power of network-based differential analysis to automation scripts. Copycat aims to enable Cytoscape users to compare and contrast networks by highlighting and arranging nodes not common to both networks, and by showing both networks using the same layout, scale and placement. With a few extra REST calls, scripts can discover nodes present in one network but not in the other, which can feed into more complex analyses (e.g., modifying mismatched nodes based on new data, then re-running the layout to highlight additional network changes).ġ (hereafter “Copycat”) is an evolution of the existing layoutSaver appĢ, a visual network aligner that maps node locations from one network view (called the source) to another (called the target). Copycat enables researchers to visually compare groups of homologous genes, generate network comparison images for publications, and quickly identify differences between similar networks at a glance without leaving their script. With the advent of Cytoscape Automation (packaged in Cytoscape v3.6.0), researchers can utilize the Copycat layout and its output in workflows written in their language of choice by using only a few simple REST calls. Copycat addresses these issues and provides additional layout options. LayoutSaver cloned a network layout by mapping node locations from one network to another based on node attribute values, but failed to clone view scale and location, and provided no means of identifying which nodes were successfully mapped between networks. The copycatLayout app is a network-based visual differential analysis tool that improves upon the existing layoutSaver app and is delivered pre-installed with Cytoscape, beginning with v3.6.0.
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