Contents
Clustering module¶
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class
ClusterNode
(newick=None, text_array=None, fdist=<function spearman_dist>)¶ Bases:
ete2.coretype.tree.TreeNode
Creates a new Cluster Tree object, which is a collection of ClusterNode instances connected in a hierarchical way, and representing a clustering result.
a newick file or string can be passed as the first argument. An ArrayTable file or instance can be passed as a second argument.
- Examples:
- t1 = Tree() # creates an empty tree t2 = Tree( ‘(A:1,(B:1,(C:1,D:1):0.5):0.5);’ ) t3 = Tree( ‘/home/user/myNewickFile.txt’ )
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get_dunn
(clusters, fdist=None)¶ Calculates the Dunn index for the given set of descendant nodes.
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get_leaf_profiles
()¶ Returns the list of all the profiles associated to the leaves under this node.
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get_silhouette
(fdist=None)¶ Calculates the node’s silhouette value by using a given distance function. By default, euclidean distance is used. It also calculates the deviation profile, mean profile, and inter/intra-cluster distances.
- It sets the following features into the analyzed node:
- node.intracluster
- node.intercluster
- node.silhouete
intracluster distances a(i) are calculated as the Centroid Diameter
intercluster distances b(i) are calculated as the Centroid linkage distance
** Rousseeuw, P.J. (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math., 20, 53-65.
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iter_leaf_profiles
()¶ Returns an iterator over all the profiles associated to the leaves under this node.
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link_to_arraytable
(arraytbl)¶ Allows to link a given arraytable object to the tree structure under this node. Row names in the arraytable object are expected to match leaf names.
Returns a list of nodes for with profiles could not been found in arraytable.
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set_distance_function
(fn)¶ Sets the distance function used to calculate cluster distances and silouette index.
ARGUMENTS:
fn: a pointer to python function acepting two arrays (numpy) as arguments.EXAMPLE:
# A simple euclidean distance my_dist_fn = lambda x,y: abs(x-y) tree.set_distance_function(my_dist_fn)
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ClusterTree
¶ alias of
ClusterNode