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