evcouplings.visualize package

evcouplings.visualize.misc module

evcouplings.visualize.mutations module

evcouplings.visualize.pairs module

evcouplings.visualize.parameters module

Visualization of pair model parameters

Authors:
Thomas A. Hopf
evcouplings.visualize.parameters.evzoom_data(model, ec_threshold=0.9, freq_threshold=0.01, Jij_threshold=10, score='cn', reorder='KRHEDNQTSCGAVLIMPYFW')[source]

Generate data for EVzoom visualization. Use evzoom_json() to get final JSON string to use with EVzoom.

Parameters:
  • model (evcouplings.couplings.model.CouplingsModel) – Parameters of pairwise graphical model
  • ec_threshold (float or int, optional (default: 0.9)) – Only display evolutionary couplings above this threshold. If float between 0 and 1, this will be interpreted as probability cutoff for mixture model. Otherwise, will be interpreted as absolute number of couplings.
  • freq_threshold (float, optional (default: 0.01)) – Only display coupling parameters for amino acids with at least this frequency in the underlying sequence alignment
  • Jij_threshold (int or float, optional (default: 10)) – Only display coupling parameters above this threshold. If float, this number will be interpreted as an actual score threshold; if int, this will be interpreted as a percentage of the maximum absolute score.
  • score (str, optional (default: "cn")) – Use this score to determine which couplings to display. Valid choices are the score columns contained in the CouplingsModel.ecs dataframe
  • reorder (str, optional (default: "KRHEDNQTSCGAVLIMPYFW")) – Order of amino acids in displayed coupling matrices
Returns:

  • map_ (dict) – Map containing sequence indices and characters
  • logo (list) – List containing information about sequence logos for axes of visualization
  • matrix (dict) – List containing couplings that will be visualized

evcouplings.visualize.parameters.evzoom_json(model, **kwargs)[source]

Create JSON input for visualizing parameters of pairwise graphical model using EVzoom

Parameters:
Returns:

EVzoom-ready JSON input

Return type:

str

evcouplings.visualize.pymol module