biom.table.Table.sort

Table.sort(sort_f=<function natsort>, axis='sample')

Return a table sorted along axis

Parameters:

sort_ffunction, optional

Defaults to biom.util.natsort. A function that takes a list of values and sorts it

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

The axis to operate on

Returns:

biom.Table

A table whose samples or observations are sorted according to the sort_f function

Examples

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

Create a 2x3 BIOM table:

>>> data = np.asarray([[1, 0, 4], [1, 3, 0]])
>>> table = Table(data, ['O2', 'O1'], ['S2', 'S1', 'S3'])
>>> print(table) 
# Constructed from biom file
#OTU ID S2  S1  S3
O2  1.0 0.0 4.0
O1  1.0 3.0 0.0

Sort the order of samples in the table using the default natural sorting:

>>> new_table = table.sort()
>>> print(new_table) 
# Constructed from biom file
#OTU ID S1  S2  S3
O2  0.0 1.0 4.0
O1  3.0 1.0 0.0

Sort the order of observations in the table using the default natural sorting:

>>> new_table = table.sort(axis='observation')
>>> print(new_table) 
# Constructed from biom file
#OTU ID S2  S1  S3
O1  1.0 3.0 0.0
O2  1.0 0.0 4.0

Sort the samples in reverse order using a custom sort function:

>>> sort_f = lambda x: list(sorted(x, reverse=True))
>>> new_table = table.sort(sort_f=sort_f)
>>> print(new_table)  
# Constructed from biom file
#OTU ID S3  S2  S1
O2  4.0 1.0 0.0
O1  0.0 1.0 3.0