Abstract
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. 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. Copycat addresses these issues and provides additional layout options. 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 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 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).
Highlights
The copycatLayout app[1] is an evolution of the existing layoutSaver app[2], a visual network aligner that maps node locations from one network view to another
Using a hashmap to store node attributes and locations within solely the source network allows Copycat layout to run in O(N+M) time while only requiring O(N) memory, where N is the number of nodes in the source network and M is the number of nodes in the target network
It is important to note that the Commands endpoint is automatically generated by Cytoscape Tunables and is meant to be used via Cytoscape Command Tools, whereas the CyREST Functions are crafted by the developer for use in Python- and R-based automation scripts
Summary
1. Bernhard Mlecnik , Cordelier Research Center, Paris, France Inovarion, Paris, France. 2. Katja Luck , Dana–Farber Cancer Institute, Boston, USA Dana–Farber Cancer Institute, Boston, USA Harvard Medical School, Boston, USA. Any reports and responses or comments on the article can be found at the end of the article. This article is included in the International Society for Computational Biology Community Journal gateway. This article is included in the Cytoscape gateway. This revision aims to address the comments of the reviewers. We added details to the Operation section on applying Copycat Layout from the Cytoscape Desktop interface, and added more future plans for handling mappings that are not one-to-one. The double quotes in the JSON code have been changed to be consistent with the rest of the code sections.
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