biom.table.Table.metadata_to_dataframe

Table.metadata_to_dataframe(axis)

Convert axis metadata to a Pandas DataFrame

Parameters:

axis{‘sample’, ‘observation’}

The axis to operate on.

Returns:

pd.DataFrame

A DataFrame indexed by the ids of the desired axis, columns by the metadata keys over that axis.

Raises:

UnknownAxisError

If the requested axis isn’t recognized

KeyError

IF the requested axis does not have metadata

TypeError

If a metadata column is a list or tuple, but is jagged over the axis.

Notes

Nested metadata (e.g., KEGG_Pathways) is not supported.

Metadata which are lists or tuples (e.g., taxonomy) are expanded such that each index position is a unique column. For instance, the key taxonomy will become “taxonomy_0”, “taxonomy_1”, etc where “taxonomy_0” corresponds to the 0th index position of the taxonomy.

Examples

>>> from biom import example_table
>>> example_table.metadata_to_dataframe('observation')
   taxonomy_0     taxonomy_1
O1   Bacteria     Firmicutes
O2   Bacteria  Bacteroidetes