ReportGenerator

class visual.ReportGenerator.ReportGenerator(base_file_html_path: str = './visual/web/base.html')[source]

Bases: object

Generate interactive HTML reports for protein-protein interaction (PPI) networks.

This class creates standalone HTML reports with embedded Cytoscape.js visualizations and analysis plots. Reports include interactive controls for selecting which node/edge attributes determine visual properties (color, size, width).

html_template

The base HTML template with placeholders for dynamic content.

Type:

str

add_cytoscape_html_report(network: PPINetwork, title: str = 'Protein Network Report', node_color_attr: str = 'pagerank', node_size_attr: str = 'degree', edge_width_attr: str = 'combined_score', cmap_name: str = 'viridis', min_node_size: float = 35, max_node_size: float = 100, min_edge_width: float = 1, max_edge_width: float = 10) → ReportGenerator[source]

Add an interactive Cytoscape.js network visualization to the report.

The visualization includes dropdown menus for dynamically selecting which node/edge attributes control color, size, and width, allowing interactive exploration of different network properties.

Parameters:

  • network – The PPINetwork object to visualize.

  • title – Title for the network report. Defaults to “Protein Network Report”.

  • node_color_attr – Node attribute to control node color. Defaults to “pagerank”.

  • node_size_attr – Node attribute to control node size. Defaults to “degree”.

  • edge_width_attr – Edge attribute to control edge width. Defaults to “combined_score”.

  • cmap_name – Name of the matplotlib colormap. Defaults to “viridis”.

  • min_node_size – Minimum node size in pixels. Defaults to 35.

  • max_node_size – Maximum node size in pixels. Defaults to 100.

  • min_edge_width – Minimum edge width in pixels. Defaults to 1.

  • max_edge_width – Maximum edge width in pixels. Defaults to 10.

Returns:

Self for method chaining.

Return type:

ReportGenerator

Note

The generated HTML tries to load cytoscape.min.js locally first. If not found, it loads Cytoscape.js from the online CDN.

add_section(html_to_add: str) → ReportGenerator[source]

Add a new section to the HTML report.

Adds the provided HTML content by replacing the placeholder string.

Parameters:

html_to_add – HTML string to insert into the report.

Returns:

Self for method chaining.

Return type:

ReportGenerator

Note

The placeholder string is defined as __ADD_MORE_SECTIONS__ and should be present in the base HTML template.

add_section_from_file(file: str, replacements: Dict[str, str] | None = None) → ReportGenerator[source]

Add a new section to the HTML report by reading from an HTML file.

Optionally performs string replacements before inserting the content.

Parameters:

  • file – Path to an HTML file to read and insert.

  • replacements – Optional dictionary mapping strings to replace in the file content. Defaults to None.

Returns:

Self for method chaining.

Return type:

ReportGenerator

Raises:

  • FileNotFoundError – If the specified file does not exist.

  • IOError – If the file cannot be read.

Example

>>> gen = ReportGenerator()
>>> gen.add_section_from_file(
...     file="./plots.html",
...     replacements={"__PLOT_1__": encoded_image_1, "__PLOT_2__": encoded_image_2}
... )
generate_report_file(output_file: str = 'protein_network_report.html') → str[source]

Generate and save the final HTML report file.

Parameters:

output_file – Output file path for the HTML report. Defaults to “protein_network_report.html”.

Returns:

The absolute path to the generated report file.

Return type:

str

Raises:

IOError – If the report file cannot be written.