Package igraph :: Module clustering :: Class Dendrogram

Class Dendrogram

object --+    
         |    
Clustering --+
             |
            Dendrogram

Known Subclasses:: VertexDendrogram

The hierarchical clustering (dendrogram) of some dataset.

A hierarchical clustering means that we know not only the way the elements are separated into groups, but also the exact history of how individual elements were joined into larger subgroups.

This class internally represents the hierarchy by a matrix with n rows and 2 columns -- or more precisely, a list of lists of size 2. This is exactly the same as the original format used by igraph's C core. The ith row of the matrix contains the indices of the two clusters being joined in time step i. The joint group will be represented by the ID n+i, with i starting from one. The ID of the joint group will be referenced in the upcoming steps instead of any of its individual members. So, IDs less than or equal to n (where n is the number of rows in the matrix) mean the original members of the dataset (with ID from 0 to n), while IDs up from n+1 mean joint groups. As an example, take a look at the dendrogram and the internal representation of a given clustering of five nodes:

 0 -+
    |
 1 -+-+
      |
 2 ---+-+        <====>   [[0, 1], [3, 4], [2, 5], [6, 7]]
        |
 3 -+   |
    |   |
 4 -+---+---

Instance Methods

[hide private]

__init__(self, merges)
Creates a hierarchical clustering.

__plot__(self, context, bbox, palette, *args, **kwds)
Draws the dendrogram on the given Cairo context

__str__(self)
str(x)

_convert_matrix_to_tuple_repr(merges, n=None)

_get_merges(self)

_item_box_size(self, context, horiz, idx)
Calculates the amount of space needed for drawing an individual vertex at the bottom of the dendrogram.

_plot_item(self, context, horiz, idx, x, y)

_traverse_inorder(self)
Conducts an inorder traversal of the merge tree.

summary(self)
Draws the dendrogram of the hierarchical clustering in a string

Inherited from Clustering: __getitem__, __len__, size, size_histogram, sizes

Inherited from Clustering (private): _get_membership

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Properties

[hide private]

merges
The performed merges in matrix format

Inherited from Clustering: membership

Inherited from object: __class__

Method Details

[hide private]

init(self, merges)
(Constructor)

Creates a hierarchical clustering.

Parameters:

merges - the merge history either in matrix or tuple format

Overrides: Clustering.__init__

plot(self, context, bbox, palette, *args, **kwds)

Draws the dendrogram on the given Cairo context

Supported keyword arguments are:

orientation: the orientation of the dendrogram. Must be one of the following values: left-right, bottom-top, right-left or top-bottom. Individual elements are always placed at the former edge and merges are performed towards the latter edge. Possible aliases: horizontal = left-right, vertical = bottom-top, lr = left-right, rl = right-left, tb = top-bottom, bt = bottom-top. The default is left-right.

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

_convert_matrix_to_tuple_repr(merges, n=None)

None

_get_merges(self)

None

_item_box_size(self, context, horiz, idx)

Calculates the amount of space needed for drawing an individual vertex at the bottom of the dendrogram.

_plot_item(self, context, horiz, idx, x, y)

None

_traverse_inorder(self)

Conducts an inorder traversal of the merge tree.

The inorder traversal returns the nodes on the last level in the order they should be drawn so that no edges cross each other.

Returns:: the result of the inorder traversal in a list.

summary(self)

Draws the dendrogram of the hierarchical clustering in a string

Property Details

[hide private]

merges

The performed merges in matrix format

Get Method:: igraph.clustering.Dendrogram._get_merges(self)

Set Method:

None

Delete Method:

None

Class Dendrogram

__init__(self, merges) (Constructor)

__plot__(self, context, bbox, palette, *args, **kwds)

__str__(self) (Informal representation operator)

_convert_matrix_to_tuple_repr(merges, n=None)

_get_merges(self)

_item_box_size(self, context, horiz, idx)

_plot_item(self, context, horiz, idx, x, y)

_traverse_inorder(self)

summary(self)

merges

init(self, merges)
(Constructor)

plot(self, context, bbox, palette, *args, **kwds)

str(self)
(Informal representation operator)