liana.resource.translate_resource

liana.resource.translate_resource#

liana.resource.translate_resource(resource, map_df, columns=None, **kwargs)#

Generate orthologs for multiple columns in a DataFrame.

Parameters:

  • resource (DataFrame) – Input DataFrame.

  • map_df (DataFrame) – DataFrame with orthology mappings, where the first column is the source and the second column is the target for mapping.

  • columns (list[str] (default: None)) – List of column names to translate.

  • **kwargs – Additional arguments for liana.utils.translate_column.

Return type:

DataFrame

Returns:

Resulting DataFrame with translated columns.

Examples

Translates the 'ligand' and 'receptor' columns in one go. In practice map_df comes from liana.resource.get_hcop_orthologs(); interactions whose partners have no ortholog are dropped:

>>> import pandas as pd
>>> import liana as li
>>> resource = li.rs.select_resource('consensus').head(3)
>>> map_df = pd.DataFrame({'source': ['LGALS9', 'PTPRC', 'MET', 'CD44'],
...                        'target': ['Lgals9', 'Ptprc', 'Met', 'Cd44']})
>>> li.rs.translate_resource(resource, map_df)
   ligand receptor
0  Lgals9    Ptprc
1  Lgals9      Met
2  Lgals9     Cd44