decoupler.translate_net

decoupler.translate_net(net, source='source', target='target', source_tax_id=9606, target_tax_id=10090, id_type='genesymbol', translate_source=False)

Translate networks between species by orthology.

This function downloads orthology databases from omnipath and converts genes between species. The first time you run this function will take a while (~15 minutes) but then it stores all the information in cache for quick reusability.

In case you need to restart the cache, you can do it by doing: rm -r .pypath/cache/

Parameters:

netDataFrame

Network in long format.

sourcestr

Column name in net with source nodes.

targetstr

Column name in net with target nodes.

source_tax_idint

NCBI Taxonomy ID of the source organism.

target_tax_idint

NCBI Taxonomy ID of the target organism.

id_type: str

Identifier type of the source and target columns. Can be “genesymbol”, “uniprot”, “ensmbl”

translate_sourcebool

Whether to also translate the source column in net.

Returns:

hom_netDataFrame

Network in long format with translated genes.