Export a ComplexMap Network for External Tools

Exports the `ComplexMap` nodes and edges to compatible file formats, preserving systems biology attributes like Specificity Scores and Functional Domains.

Usage

exportNetwork(
  complexMapObject,
  filePrefix,
  format = "cytoscape",
  verbose = TRUE
)

Arguments

complexMapObject

A `ComplexMap` object.

filePrefix

Character string for output filenames (e.g., "results/my_map").

format

Output format. One of: - `"cytoscape"`: Writes separate node and edge TSV files for Cytoscape Desktop. - `"graphml"`: Writes a GraphML file (via `igraph`). - `"tsv"`: Writes a single node-attribute TSV file.

verbose

Logical.

Value

None (Writes files to disk).

Details

**Systems Biology Rationale:** To verify the landscape in external tools (e.g., Cytoscape Desktop), this function ensures that the specific calculated attributes are correctly formatted:

- **`score`**: The Specificity Score. - **`primaryFunctionalDomain`**: The Specific Label. - **`colorHex`**: The calculated blended color.

It performs a "Sanitization" step to convert any R-specific list columns into semi-colon separated strings and fills `NA` values to ensure safe import.

Author

Qingzhou Zhang <zqzneptune@hotmail.com>