biosimulators_utils.viz.vega.ginml package#

Submodules#

biosimulators_utils.viz.vega.ginml.core module#

Utility for converting activity flow diagrams from GINsim Markup Language (GINML) to Vega format

Author:: Andrew Freiburger <afreiburger@uvic.ca>
Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-07-23
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.viz.vega.ginml.core.ginml_to_vega(node_values_data_set, ginml_filename, vega_filename, optimum_nodes_quantity=18, edge_x_value_adjustment=0, edge_y_value_adjustment=45, signal_height=65, signal_padding=10, indent=2)[source]#

Convert an activity flow diagram from GINsim Markup Language (GINML) format to Vega format.

Parameters:

node_values_data_set (dict) –
Vega data set with the predicted values of each node. The dictionary should have one of the following schemas
- Contain a key values whose value is a list of the predicted node values. Each item of the list should be a dictionary with two keys
  - label: value should be the SBML-qual identifier of the corresponding node
  - values: array of the predicted value of the species at each time step
- Contain a key url whose value is a URL where the predicted values can be retrieved in JSON format. The data should be in the same format outlined above.
- Contain a key sedmlUri whose value is an array which contains two elements that indicate
  - The location of the SED-ML file (within its parent COMBINE/OMEX archive) which will produce the predictions for the visualization
  - The id of the SED-ML report which will contain the predictions for the visualization
ginml_filename (str) – path to the visualization in GINML format
vega_filename (str) – path to save the visualization in Vega format
optimum_nodes_quantity (int)
edge_x_value_adjustment (int)
edge_y_value_adjustment (int)
signal_height (int)
signal_padding (int)
indent (int or None, optional) – indentation