skbio.table.example_table#
- skbio.table.example_table = 2 x 3 <class 'biom.table.Table'> with 5 nonzero entries (83% dense)[source]#
The (canonically pronounced ‘teh’) Table.
Give in to the power of the Table!
Creates an in-memory representation of a BIOM file. BIOM version 1.0 is based on JSON to provide the overall structure for the format while versions 2.0 and 2.1 are based on HDF5. For more information see [1] and [2]
- Parameters:
- dataarray_like
An (N,M) sample by observation matrix represented as one of these types: * An 1-dimensional array of values * An n-dimensional array of values * An empty list * A list of numpy arrays * A list of dict * A list of sparse matrices * A dictionary of values * A list of lists * A sparse matrix of values
- observation_idsarray_like of str
A (N,) dataset of the observation IDs, where N is the total number of IDs
- sample_idsarray_like of str
A (M,) dataset of the sample IDs, where M is the total number of IDs
- observation_metadatalist of dicts, optional
per observation dictionary of annotations where every key represents a metadata field that contains specific metadata information, ie taxonomy, KEGG pathway, etc
- sample_metadataarray_like of dicts, optional
per sample dictionary of annotations where every key represents a metadata field that contains sample specific metadata information, ie
- table_idstr, optional
A field that can be used to identify the table
- typestr, see notes
The type of table represented
- create_datestr, optional
Date that this table was built
- generated_bystr, optional
Individual who built the table
- observation_group_metadatalist, optional
group that contains observation specific group metadata information (e.g., phylogenetic tree)
- sample_group_metadatalist, optional
group that contains sample specific group metadata information (e.g., relationships between samples)
- Attributes:
- shape
- dtype
- nnz
- matrix_data
- type
- table_id
- create_date
- generated_by
- format_version
- Raises:
- TableException
When an invalid table type is provided.
Notes
Allowed table types are None, “OTU table”, “Pathway table”, “Function table”, “Ortholog table”, “Gene table”, “Metabolite table”, “Taxon table”
References
[2]D. McDonald, et al. “The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome” GigaScience 2012 1:7