biom.table.Table.sum

Table.sum(axis='whole')

Returns the sum by axis

Parameters:

axis{‘whole’, ‘sample’, ‘observation’}, optional

The axis on which to operate.

Returns:

numpy.array or float

If axis is “whole”, returns an float representing the whole table sum. If axis is either “sample” or “observation”, returns a numpy.array that holds a sum for each sample or observation, respectively.

Examples

>>> import numpy as np
>>> from biom.table import Table

Create a 2x3 BIOM table:

>>> data = np.asarray([[0, 0, 1], [1, 3, 42]])
>>> table = Table(data, ['O1', 'O2'], ['S1', 'S2', 'S3'])

Add all values in the table:

>>> table.sum()
array(47.0)

Add all values per sample:

>>> table.sum(axis='sample') 
array([  1.,  3.,  43.])

Add all values per observation:

>>> table.sum(axis='observation') 
array([  1.,  46.])