biosimulators_utils.viz.vega.escher package#

Submodules#

biosimulators_utils.viz.vega.escher.core module#

Utility for converting metabolic maps from Escher to Vega format

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-02-06
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.viz.vega.escher.core.escher_to_vega(reaction_fluxes_data_set, escher_filename, vega_filename, max_width_height=800, legend_padding=20, legend_width=40, signal_height=20, arrow_head_gap=16.0, indent=2, metabolic_map_data_file=None)[source]#

Convert a metabolic pathway map from Escher format to Vega format.

Parameters:

reaction_fluxes_data_set (dict) –
Vega data set with each predicted reaction flux. The dictionary should have one of the following schemas
- Contain a key values whose value is a list of the predicted flux values. Each predicted flux value should be a dictionary with two keys
  - label: value should be the BiGG identifier of the corresponding reaction
  - values: array with a single value equal to the predicted flux
- Contain a key url whose value is a URL where the predicted flux 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 flux predictions for the visualization
  - The id of the SED-ML report which will contain the flux predictions for the visualization
escher_filename (str) – path to the visualization in Escher format
vega_filename (str) – path to save the visualization in Vega format
max_width_height (int, optional) – maximum height/width of the metabolic map in pixels
legend_padding (int, optional) – horizontal spacing between the metabolic map and legend in pixels
legend_width (int, optional) – legend width in pixels, including the width of the title
signal_height (int, optional) – height of signals in pixels
arrow_head_gap (float, optional) – spacing between arrow heads and nodes
indent (int or None, optional) – indentation
metabolic_map_data_file (dict or None, optional) – If None, store the data for the metabolic map (e.g., coordinates of metabolites, reactions) inline within the generated Vega file. If not None, store the data for the metabolic map in a separate file to be loaded via a URL. In this case, the argument must be a dictionary which two keys, filename and url which indicate where the data should be saved and where this file will be hosted.

biosimulators_utils.viz.vega.escher.core.read_escher_map_config(filename)[source]#

Read the configuration of an Escher map from a file

Parameters:: filename (str) – path to a configuration of an Escher map
Returns:: configuration of an Escher map
Return type:: list