ecoli.analysis.single.selected_fluxes

ecoli.analysis.single.selected_fluxes.esc_latex(s)[source]

Helper function to escape a string for LaTeX.

ecoli.analysis.single.selected_fluxes.plot(params, conn, history_sql, config_sql, success_sql, sim_data_paths, validation_data_paths, outdir, variant_metadata, variant_names)[source]

All options have default values (do not need to be explicitly provided).

Parameters:

  • params (dict[str, Any]) –

    Dictionary of parameters given under analysis name in configuration JSON. Config options look like this:

    {

    // show_enzyme_counts: whether to show enzyme counts along with fluxes
    "show_enzyme_counts": true,

    // Height of each row and width of each column in inches.
    // Defaults to 3 and 4 inches, respectively.
    // Overidden if "figsize" is provided!
    "row_height": 3,
    "col_width": 4,

    // figsize: custom figure size
    "figsize": [12, 9],

    // plot_reactions: list of reaction-sets to plot in each row.
    "plot_reactions" : [
        // "Reaction-sets" can be:
        // (1) single strings, for the ID of a single reaction
        "PGLUCISOM-RXN",

        // (2) lists of string IDs
        ["3PGAREARR-RXN", "RXN-15513"],

        // (3) dictionaries of string IDs paired with human-readable labels
        {"PEPDEPHOS-RXN" : "PEP kinase", "PEPSYNTH-RXN": "PEP synthase"}
    ]
}

  • conn (DuckDBPyConnection)

  • history_sql (str)

  • config_sql (str)

  • success_sql (str)

  • sim_data_paths (dict[str, dict[int, str]])

  • validation_data_paths (list[str])

  • outdir (str)

  • variant_metadata (dict[str, dict[int, Any]])

  • variant_names (dict[str, str])