TreeNode.
from_taxonomy
(lineage_map)[source]¶Construct a tree from a taxonomy
State: Experimental as of 0.4.0.
lineage_map (iterable of tuple) – A id to lineage mapping where the first index is an ID and the second index is an iterable of the lineage.
The constructed taxonomy
Examples
>>> from skbio.tree import TreeNode
>>> lineages = [
... ('1', ['Bacteria', 'Firmicutes', 'Clostridia']),
... ('2', ['Bacteria', 'Firmicutes', 'Bacilli']),
... ('3', ['Bacteria', 'Bacteroidetes', 'Sphingobacteria']),
... ('4', ['Archaea', 'Euryarchaeota', 'Thermoplasmata']),
... ('5', ['Archaea', 'Euryarchaeota', 'Thermoplasmata']),
... ('6', ['Archaea', 'Euryarchaeota', 'Halobacteria']),
... ('7', ['Archaea', 'Euryarchaeota', 'Halobacteria']),
... ('8', ['Bacteria', 'Bacteroidetes', 'Sphingobacteria']),
... ('9', ['Bacteria', 'Bacteroidetes', 'Cytophagia'])]
>>> tree = TreeNode.from_taxonomy(lineages)
>>> print(tree.ascii_art())
/Clostridia-1
/Firmicutes
| \Bacilli- /-2
/Bacteria|
| | /-3
| | /Sphingobacteria
| \Bacteroidetes \-8
| |
---------| \Cytophagia-9
|
| /-4
| /Thermoplasmata
| | \-5
\Archaea- /Euryarchaeota
| /-6
\Halobacteria
\-7