matchms.networking.networking_functions module

Helper functions to build and handle spectral networks

matchms.networking.networking_functions.get_top_hits(scores: <module 'matchms.Scores' from '/home/docs/checkouts/readthedocs.org/user_builds/matchms/checkouts/fix_readthedocs/matchms/Scores.py'>, identifier_key: str = 'spectrum_id', top_n: int = 25, search_by: str = 'queries', score_name: str = None, ignore_diagonal: bool = False) → Tuple[dict, dict]

Get top_n highest scores (and indices) for every entry.

Parameters:

• scores – Matchms Scores object containing all similarities.

• identifier_key – Metadata key for unique intentifier for each spectrum in scores. Will also be used for the naming the network nodes. Default is ‘spectrum_id’.

• top_n – Return the indexes and scores for the top_n highest scores. Scores between a spectrum with itself (diagonal of scores.scores) will not be taken into account.

• search_by – Chose between ‘queries’ or ‘references’ which decides if the top_n matches for every spectrum in scores.queries or in scores.references will be collected and returned.

• score_name – Name of the score that should be used (if scores contains multiple different scores).

• ignore_diagonal – Set to True if scores.scores is symmetric (i.e. if references and queries were the same) and if scores between spectra with themselves should be excluded.

matchms.networking.networking_functions.get_top_hits_by_query(scores: <module 'matchms.Scores' from '/home/docs/checkouts/readthedocs.org/user_builds/matchms/checkouts/fix_readthedocs/matchms/Scores.py'>, identifier_key: str, top_n: int, score_name: str, ignore_diagonal: bool) → Tuple[dict, dict]

Get the top hits in the network from the “query” spectra perspective

Args:

scores (Scores): scores matrix from which to extract the hits identifier_key (str): Key to use as identifier for the spectra top_n (int): N for the number of spectra to retrieve. score_name (str): Name of the score to retrieve ignore_diagonal (bool): Whether to ignore self hits on the diagonal or not.

Returns:

dict, dict: Dictionaries of indices and scores.

matchms.networking.networking_functions.get_top_hits_by_references(scores: <module 'matchms.Scores' from '/home/docs/checkouts/readthedocs.org/user_builds/matchms/checkouts/fix_readthedocs/matchms/Scores.py'>, identifier_key: str, top_n: int, score_name: str, ignore_diagonal: bool) → Tuple[dict, dict]

Get the top hits from the scoring by “references”. This function differs only slightly from the one by query.

Args:

scores (Scores): Scores from which to retrieve the queries. identifier_key (str): Key to use as identifier for the spectra. top_n (int): N for the top N to receive. score_name (str): Score name to retrieve the top hits from. ignore_diagonal (bool): Whether to ignore self matches on the diagonal.

Returns:

dict, dict: Dictionaries of indices and scores.