Crosslink

Crosslink visualizes grouped-node biological networks in R to represent and annotate relationships in gene regulatory, drug-target, ligand-receptor, and multi-omics association data.

Key Features:

• Metadata Management: The CrossLink class stores and manages extensive metadata for nodes and edges in a network.
• Node Coordinate Manipulation: Node coordinates and node groups can be transformed using affine transformation and function mapping transformations.
• Predefined Network Layouts: Provides row, column, arc, polygon, and hive layouts that can be customized and combined within a single diagram.
• ggplot2 Integration: Includes a wrapper to draw network connections with ggplot2, enabling aesthetic mappings of metadata and addition of related annotation graphs.

Scientific Applications:

• Gene regulatory networks: Visualization of relationships and groupings in gene regulatory network analyses.
• Drug-target interactions: Representation and annotation of drug-target interaction networks.
• Ligand-receptor dynamics: Visualization of ligand-receptor pairings and their group-wise relationships.
• Multi-omics association networks: Display and annotation of associations across multi-omics datasets.

Methodology:

Data are stored in the CrossLink class; node coordinates are adjusted via affine and function mapping transformations; predefined row, column, arc, polygon, and hive layouts can be customized and combined; visualization uses ggplot2 for drawing connections, aesthetic mappings, and annotation graphs.