Source code for evcouplings.visualize.parameters

Visualization of pair model parameters

  Thomas A. Hopf

import json
import numpy as np
from evcouplings.couplings.pairs import add_mixture_probability

[docs]def evzoom_data(model, ec_threshold=0.9, freq_threshold=0.01, Jij_threshold=10, score="cn", reorder="KRHEDNQTSCGAVLIMPYFW"): """ 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 """ DIGITS = 2 DIGITS_LOGO = 2 ecs = model.ecs if 0 < ec_threshold <= 1.0: ecs = add_mixture_probability(ecs, score=score) ecs_sel = ecs.loc[ecs.probability >= ec_threshold] else: ecs_sel = ecs.iloc[:int(ec_threshold)] # if cutoff for couplings is given as int, interpret # as percentage of biggest absolute coupling value if isinstance(Jij_threshold, int): max_val = np.max(np.abs(model.Jij())) Jij_threshold = max_val * Jij_threshold / 100 if reorder is not None: alphabet = np.array(list(reorder)) alphabet_order = [ model.alphabet_map[c] for c in reorder ] else: alphabet = model.alphabet alphabet_order = sorted( model.alphabet_map.values() ) # Map containing sequence and indeces map_ = { "letters": "".join(model.seq()), "indices": list(map(int,, } # assemble coupling matrix matrix = [] for idx, r in ecs_sel.iterrows(): i, j, score_ij = r["i"], r["j"], r[score] Jij = model.Jij(i, j)[alphabet_order, :][:, alphabet_order] ai_set = np.where( np.max(np.abs(Jij), axis=1) > Jij_threshold )[0] aj_set = np.where( np.max(np.abs(Jij), axis=0) > Jij_threshold )[0] cur_matrix = [ [round(Jij[ai, aj], DIGITS) for aj in list(aj_set)] for ai in list(ai_set) ] cur_matrix_T = [ [round(Jij[ai, aj], DIGITS) for ai in list(ai_set)] for aj in list(aj_set) ] cur_row = { "i": + 1, "j": + 1, "score": round(score_ij, DIGITS), "iC": "".join(alphabet[ai_set]), "jC": "".join(alphabet[aj_set]), "matrix": cur_matrix, } cur_row_T = { "i": cur_row["j"], "j": cur_row["i"], "score": cur_row["score"], "iC": cur_row["jC"], "jC": cur_row["iC"], "matrix": cur_matrix_T, } matrix.append(cur_row) matrix.append(cur_row_T) # assemble sequence logo fi = q = model.num_symbols B = -fi * np.log2(fi) B[fi <= 0] = 0 R = np.log2(q) - B.sum(axis=1) logo = [] for i in range(model.L): order = np.argsort(fi[i, :]) frequent = order[fi[i, order] >= freq_threshold] symbols = model.alphabet[frequent] fi_row = fi[i, frequent] * R[i] logo.append([ {"code": s, "bits": round(float(h), DIGITS_LOGO)} for s, h in zip(symbols, fi_row) ]) return map_, logo, matrix
[docs]def evzoom_json(model, **kwargs): """ Create JSON input for visualizing parameters of pairwise graphical model using EVzoom Parameters ---------- model : evcouplings.couplings.model.CouplingsModel Parameters of pairwise graphical model **kwargs See evzoom_data() for options Returns ------- str EVzoom-ready JSON input """ map_, logo, matrix = evzoom_data(model, **kwargs) data = { "map": map_, "logo": logo, "couplings": matrix, } return json.dumps(data)