micom.taxonomy

Helpers to convert external data to a MICOM taxonomy.

Module Contents

Functions

build_from_qiime(abundance, taxonomy: pandas.Series, collapse_on='genus') → pandas.DataFrame

Build the specification for the community models.

qiime_to_micom(feature_table, taxonomy, collapse_on='genus')

Load a micom taxonomy from Qiime 2 data.

micom.taxonomy.build_from_qiime(abundance, taxonomy: pandas.Series, collapse_on='genus') pandas.DataFrame[source]

Build the specification for the community models.

micom.taxonomy.qiime_to_micom(feature_table, taxonomy, collapse_on='genus')[source]

Load a micom taxonomy from Qiime 2 data.

Parameters
  • feature_table (str) – Path to a Qiime 2 FeatureTable artifact.

  • taxonomy (str) – Path to a Qiime 2 FeatureData[Taxonomy] artifact.

  • collapse_on (str or List[str]) – The taxa ranks to collapse on. This will dictate how strict the database matching will be as well.

Returns

A micom taxonomy containing abundances and taxonomy calls in long format.

Return type

pd.DataFrame