Load a set of Napistu files
Arguments
- napistu_config
A napistu configuration object of class `napistu_config` containing all necessary configuration settings for the loading required assets and configuring and/or using an exiting appropriate Python environment. This config can be read from a yaml file using load_napistu_config or directly specified in R using create_napistu_config. Contains:
- python_config
A shallow list defining the Python environment. See validate_python_config
- assets_config
A shallow list defining the Napistu assets to use. See validate_assets_config
- created_at
Time stamp
- python_list
A list containing reticulate bindings to Python packages and summaries of the Python environment.
- python_modules
A named list of Python modules: `napistu`
- python_environment
- verbose
Logical scalar; if TRUE (default), prints informative messages about the current operation progress. If FALSE, runs silently.
Value
A list containing loaded assets including:
- sbml_dfs
SBML_dfs - the core pathway representation of the Napistu Python library
- napistu_graph
Network graph - a Python igraph subclass with Napistu-specific attributes and methods
- species_identifiers
Species identifier mappings
- precomputed_distances
optional, distances between species nodes
- species_names
A tibble containing the names of all genes, proteins, molecules, etc
- identifiers_nest
A tibble with one row per ontology and a nested tibble containing all the identifiers and their corresponding molecular species