copycatLayout

copycatLayout maps node column values and view geometry between network layouts within Cytoscape to enable visual differential analysis of biological networks.

Key Features:

• Enhanced Network Cloning: Maps and clones node positions along with view scale and location to preserve spatial context across network views.
• Node Mapping Identification: Identifies nodes successfully mapped between source and target networks and detects missing or unmatched nodes.
• Additional Layout Options: Provides multiple layout options to apply different spatial arrangements when transferring layouts between networks.
• Integration with Cytoscape Automation: Exposes functionality via Cytoscape Automation and REST calls to enable scripted, programmatic network comparisons.

Scientific Applications:

• Visual Comparison of Homologous Genes: Visually compares groups of homologous genes across different network views to identify conserved or divergent patterns.
• Network Comparison for Publications: Generates comparative network views suitable for inclusion in scientific publications.
• Rapid Identification of Network Differences: Provides quick visual overviews to locate differences between similar networks.

Methodology:

Maps node column values from a source network layout to a target layout while preserving view scale and location; uses Cytoscape Automation REST calls to identify nodes present in one network but absent in another; scripts can modify mismatched nodes and re-run layouts to visualize changes.