biosimulators_utils.viz.vega.sbgn package#

Submodules#

biosimulators_utils.viz.vega.sbgn.core module#

Utility for converting activity SBGN process description (PD) maps to Vega format

Author:: Andrew Freiburger <afreiburger@uvic.ca>
Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-11
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.viz.vega.sbgn.core.sbgn_pd_map_to_vega(glyph_values_data_set, sbgn_filename, vega_output_filename, max_width=700, max_height=700, indent=2)[source]#

Convert a process description (PD) map from SBGN to Vega format.

Parameters:

glyph_values_data_set (dict) –
Vega data set with the predicted dynamics of one or more glyphs. The dictionary should have one of the following schemas
- Contain a key values whose value is a list of the predicted values of the glyphs. Each element of the list should be a dictionary with two keys
  - label: value should be the SBGN label of the corresponding glyph
  - values: array of the predicted values of the glyph
- Contain a key url whose value is a URL where the predicted values of the glyphs 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 predicted values of the glyphs
  - The id of the SED-ML report which will contain the predicted values of the glyphs for the visualization
sbgn_filename (str) – the name of the SBGN file that will be parsed
vega_output_filename (str) – path to the ginsim simulation data
max_width (int) – maximum diagram width
max_height (int) – maximum diagram height
indent (int or None, optional) – indentation for exported Vega file