commitment_diagrams

commitment_diagram2image(diagram: DiGraph, fname_image: str, style_inputs: bool = True, style_edges: bool = False, style_ranks: bool = True, first_index: int = 1) → DiGraph

Creates the image file fname_image for the basin diagram given by diagram. The flag StyleInputs can be used to highlight which basins belong to which input combination. style_edges adds edge labels that indicate the size of the “border” (if compute_border was enabled in commitment_compute_diagram) and the size of the states of the source basin that can reach the target basin.

arguments:

  • diagram: a commitment diagram

  • fname_image: file name of image

  • style_inputs: whether basins should be grouped by input combinations

  • style_edges: whether edges should be size of border / reachable states

  • style_ranks: style that places nodes with the same number of reachable attractors on the same rank (level)

  • first_index: first index of attractor names

returns::

  • styled_diagram: the styled commitment diagram

example:

>>> attractors = compute_attractors(primes, update)
>>> compute_phenotype_diagram(attractors)
>>> commitment_diagram2image(diagram, "diagram.pdf")
commitment_diagrams_are_equivalent(this: DiGraph, other: DiGraph) → bool

Checks whether diagrams this and other are equivalent.

compute_commitment_diagram(attractors: dict, fname_image: Optional[str] = None, fname_json=None, edge_data=False) → DiGraph

Computes the commitment diagram for the AttrJson and STG defined in attractors, a json object computed by AttrJson_compute_json The nodes of the diagram represent states that can reach the exact same subset of attractors. Edges indicate the existence of a transition between two nodes in the respective commitment sets. Edges are labeled by the number of states of the source set that can reach the target set and, if EdgeData is true, additionally by the size of the border.

arguments:

  • attractors: json attractor data, see compute_attractors

  • fname_image: generate image for diagram

  • fname_json: save diagram as json

  • edge_data: toggles computation of additional edge data

returns::

  • diagram: the commitment diagram

example:

>>> attractors = compute_attractors(primes, update)
>>> diagram = compute_phenotype_diagram(attractors)
create_commitment_piechart(diagram: DiGraph, fname_image: str, color_map: Optional[dict] = None, title: Optional[str] = None)

Creates the commitment pie chart for the commitment diagram using matplotlib. The pieces of the chart represent states that can reach the exact same subset of Attractors.

arguments:

  • diagram: commitment diagram, see commitment_compute_diagram

  • fname_image: name of the output image

  • color_map: assignment of diagram nodes to colors for custom colors

  • title: optional title of plot

example:

>>> primes = get_primes("xiao_wnt5a")
>>> attractors = compute_attractors(primes, update)
>>> diagram = compute_commitment_diagram(attractors)
>>> create_commitment_piechart(diagram, "commitment_piechart.pdf")
open_commitment_diagram(fname_json: str) → DiGraph

Opens a commitment diagram json file. See also commitment_compute_diagram, commitment_save_diagram.

arguments:

  • fname_json: a json file name

returns:

  • diagram: the commitment diagram

example:

>>> diagram = open_commitment_diagram("commitment_diagram.json")
save_commitment_diagram(diagram: DiGraph, fname_json: str)

Saves a commitment diagram as a json file.

arguments:

  • diagram: a commitment diagram

  • fname_json: json file name

example:

>>> save_commitment_diagram(diagram, "commitment_diagram.json")