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Create Neighborhood Table

Source: R/neighborhoods.R
create_neighborhood_table.Rd

Create Neighborhood Table

Usage

create_neighborhood_table(
  napistu_list,
  species_id,
  network_type = "hourglass",
  max_steps = 3L,
  max_neighbors = 10L,
  verbose = FALSE
)

Arguments

napistu_list

A list containing loaded assets and bindings to Python modules.

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

python_modules

A named list of Python modules: `napistu`

python_environment

See validate_python_environment

napistu_config

A `napistu_config` object dictating how the `napistu_list` was initialized

loaded_at

A date-time object indicating when `napistu_list` was initialized

species_id

species identifier for focal node

network_type

what type of neighborhood should be formed (ignored if napistu_graph is undirected).

downstream

descendants of the focal node

upstream

ancestors of the focal node

hourglass

descendants and ancestors of focal node

max_steps

number of steps away from focal node allowed

max_neighbors

prune to this number of upstream regulators and downstream targets

verbose

Logical scalar; if TRUE (default), prints informative messages about the current operation progress. If FALSE, runs silently.

Value

a tibble containing one row per neighborhood with nested lists as attributes:

sc_name

A human readible name for the focal vertex

s_id

The internal unique species id of the focal vertex

c_id

The internal unique compartment id of the focal vertex

sc_id

The internal unique compartmentalized species id of the focal vertex

sc_Source

The Source object for the focal vertex

vertices

The vertices in the focal vertex's neighborhood

edges

The edges in the focal vertex's neighborhood

reaction_sources

The source pathways of the reaction vertices

Examples

setup_napistu_list(create_napistu_config())
#> 
#> ── Setting up Napistu environment ──────────────────────────────────────────────
#> No Python configuration specified, setting up conda environment
#> Using existing conda environment "napistu-env"
#> Python version 3.11 meets requirements
#> No assets configuration specified, loading bundled package data
#> ℹ Creating derived assets
#> ℹ Creating a table of species names to support lookups by name
#> ℹ Loading sbml_dfs from sbml_dfs.pkl
#> Error in value[[3L]](cond): Failed to load sbml_dfs from
#> /home/runner/work/_temp/Library/napistu.r/extdata/test_pathway/sbml_dfs.pkl:
#> ImportError:
#> /usr/share/miniconda/envs/napistu-env/lib/python3.11/lib-dynload/pyexpat.cpython-311-x86_64-linux-gnu.so:
#> undefined symbol: XML_SetAllocTrackerActivationThreshold Run
#> `reticulate::py_last_error()` for details.
species_id <- random_species(napistu_list)
#> Error: object 'napistu_list' not found

create_neighborhood_table(
    species_id,
    napistu_list = napistu_list,
    network_type = "hourglass",
    max_steps = 5L,
)
#> Error: object 'napistu_list' not found