Create Napistu Configuration
Arguments
- python_config
List describing the Python environment to use as part of the `napistu_config`. This can be the system python, a virtual environment or conda. If `python_config` is an empty list, a miniconda environment and installation can be established on-the-fly.
- virtual_env
Optional, path to a virtual environment
- conda
Optional, path to a conda executable. This can be found with `reticulate::conda_exe()`. If defined, the `conda_env_name` should also be defined.
- conda_env_name
Optional, name of the conda environment to use. A suitable environment can be created using create_conda_environment.
- python
Optional, path to a Python distribution.
- assets_config
List containing asset configuration settings as part of the `napistu_config`. If this is an empty list, the `test_pathway` bundled with `napistu-r` will be used.
- assets_dir
relative to this directory.
- sbml_dfs
Path to a pickled `SBML_dfs` object generated by the Napistu Python package. `SBML_df`s are self-contained relational representations of a pathway.
- napistu_graph
Path to a pickled `NapistuGraph` object generated by the Napistu Python package. `NapistuGraph`s are a subclass of `igraph.Graph`.
- species_identifiers
Path to a .tsv containing the systematic identifiers for all of the molecular species in the `SBML_dfs`.
- precomputed_distances
Optional, path to a .parquet file containing pairwise distances between molecular species. Defining this can speed up the calculation of shortest paths and neighborhoods.
Examples
if (FALSE) { # \dontrun{
# Direct configuration
napistu_config <- create_napistu_config(
python_config = list(virtualenv = "/path/to/venv"),
assets_config = list(
sbml_dfs = "/path/to/sbml.pkl",
napistu_graph = "/path/to/graph.pkl",
species_identifiers = "/path/to/species.tsv"
)
)
# Minimal configuration (uses defaults)
napistu_config <- create_napistu_config()
} # }