Cell Population
Base class
Bases: ABC
__init__(interaction_graph, n_cells=1, per_node_state_dim=1)
A population of independnet cells (no cell-cell interactions).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
interaction_graph |
required | ||
n_cells |
int
|
Number of independent cells in the population. |
1
|
get_derivatives(state)
Estimates derivative of system using first differences.
get_edge_set(e_type, e_type_data)
"Given an edge type, and edge data, return an edge set.
get_node_set(n_type_data)
Given node type data, return a node set with the associated attributes.
initialize_from_interaction_graph(interaction_graph)
Initializes a graph from an interaction_graph object.
Test class
Bases: CellPopulation
__init__(n_cells=1)
Information about the test interaction data
60 nodes and 57 edges. 2 different types of nodes: ['compound', 'gene']. 5 different types of interactions: ['', 'activation', 'binding/association', 'compound', 'inhibition'].
compute_decay_rates()
Applies a generic decay fn to each node type individually.
compute_production_rates()
Applies a generic production rate fn to each edge type individually.