gneiss.balances.balanceplot¶
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gneiss.balances.
balanceplot
(balances, tree, layout=None, mode='c')[source]¶ Plots balances on tree.
Parameters: - balances (np.array) – A vector of internal nodes and their associated real-valued balances. The order of the balances will be assumed to be in level order.
- tree (skbio.TreeNode) – A strictly bifurcating tree defining a hierarchical relationship between all of the features within table.
- layout (function, optional) – A layout for formatting the tree visualization. Must take a ete.tree as a parameter.
- mode (str) – Type of display to show the tree. (‘c’: circular, ‘r’: rectangular).
Notes
The tree is assumed to strictly bifurcating and whose tips match balances. It is not recommended to attempt to plot trees with a ton of leaves (i.e. more than 4000 leaves).
Examples
>>> from gneiss.balances import balanceplot >>> from skbio import TreeNode >>> tree = u"((b,c)a, d)root;" >>> t = TreeNode.read([tree]) >>> balances = [10, -10] >>> tr, ts = balanceplot(balances, t) >>> print(tr.get_ascii()) /-b /a| -root \-c | \-d
See also
skbio.TreeNode.levelorder()