(c) Copycat layout is applied, mapping the starting network layout onto the subnetwork and selecting the unmapped node that was not found in the source.Īs another example, applying Copycat layout to similar networks (i.e., rat, mouse or human) and mapping nodes by homology assignments can help verify and discover new homologous genes and gene pairs. (a) The starting network is loaded into Cytoscape and a simple layout is applied. A workflow in which transformations are documented by applying Copycat.
#Cytoscape and blast2go movie
Figure 1 illustrates a workflow that might call Copycat repeatedly to create a frame-by-frame movie of network manipulation.įigure 1.
In a workflow that performs multiple network transformations, Copycat can be used to pinpoint network differences after each transformation, thereby boosting confidence in the transformation and illuminating its real effect. The Copycat endpoint does this by invoking the Copycat layout to make common and disjoint nodes obvious and easily available to a workflow. Cytoscape Automation enables biologists to incorporate Cytoscape network visualization and analysis functionality (via REST calls) into workflows written in a language in which they are already productive (e.g., Python and R).įor example, as Cytoscape is called to transform a network (the target), it’s often important to be able to show a correspondence to an original network (the source). We upgraded Copycat to enable Cytoscape Automation 3 by exposing a new REST endpoint 4, 5, 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.
The copycatLayout app 1 (hereafter “Copycat”) is an evolution of the existing layoutSaver app 2, a visual network aligner that maps node locations from one network view (called the source) to another (called the target). 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). 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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