biom.table.Table.align_to

Table.align_to(other, axis='detect')

Align self to other over a requested axis

Parameters:

otherbiom.Table

The table to align too

axisstr, optional, {sample, observation, both, detect}

If ‘sample’ or ‘observation’, align to that axis. If ‘both’, align both axes. If ‘detect’, align what can be aligned.

Raises:

DisjointIDError

If the requested axis can’t be aligned.

UnknownAxisError

If an unrecognized axis is specified.

Examples

Align one table to another, for instance a table of 16S data to a table of metagenomic data. In this example, we’re aligning the samples of the two tables.

>>> from biom import Table
>>> import numpy as np
>>> amplicon = Table(np.array([[0, 1, 2], [3, 4, 5]]),
...                  ['Ecoli', 'Staphylococcus'],
...                  ['S1', 'S2', 'S3'])
>>> metag = Table(np.array([[6, 7, 8], [9, 10, 11]]),
...               ['geneA', 'geneB'],
...               ['S3', 'S2', 'S1'])
>>> amplicon = amplicon.align_to(metag)
>>> print(amplicon)  
# Constructed from biom file
#OTU ID S3      S2      S1
Ecoli   2.0     1.0     0.0
Staphylococcus  5.0     4.0     3.0