HiDeF Converters

HiDeF converters are designed to facilitate the transformation between CX2 and HiDeF network formats. These converters allow users to generate HiDeF-compatible files (.nodes and .edges) from hierarchical networks in CX2 format, as well as reconstruct hierarchical networks in HCX format from HiDeF data. This is particularly useful for integrating hierarchical networks into Cytoscape while maintaining structural annotations.

Example: Converting a CX2 Hierarchy to HiDeF Format

To convert a CX2 hierarchical network into HiDeF format, use the HierarchyToHiDeFConverter class:

from cellmaps_utils.hidefconverter import HierarchyToHiDeFConverter

converter = HierarchyToHiDeFConverter(input_dir="path/to/cx2_network", output_dir="path/to/output")
nodes_file, edges_file = converter.generate_hidef_files()

This will produce two files:

  • hidef_output_gene_names.nodes – containing node attributes

  • hidef_output_gene_names.edges – defining hierarchical relationships

Example: Converting HiDeF Files to an HCX Hierarchical Network

To convert HiDeF files into an HCX hierarchical network, the HiDeFToHierarchyConverter should be used.

from cellmaps_utils.hidefconverter import HiDeFToHierarchyConverter

converter = HiDeFToHierarchyConverter(
    output_dir="path/to/output",
    nodes_file_path="path/to/hidef_output_gene_names.nodes",
    edges_file_path="path/to/hidef_output_gene_names.edges",
    parent_edgelist_path="path/to/parent_network.edgelist"
)
converter.generate_hierarchy_hcx_file()

Expected Output:

  • hierarchy.cx2 – The reconstructed hierarchical network in HCX format.

  • hierarchy_parent.cx2 – The corresponding interactome (if a parent network was specified).