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 -+---+---
||Creates a hierarchical clustering.|
||Draws the dendrogram on the given Cairo context|
||Formats the dendrogram in a foreign format.|
||Sets the names of the nodes in the dendrogram|
||Returns the summary of the dendrogram.|
||Returns the performed merges in matrix format|
||Returns the names of the nodes in the dendrogram|
||Converts the matrix representation of a clustering to a tuple representation.|
||Calculates the amount of space needed for drawing an individual vertex at the bottom of the dendrogram.|
||Plots a dendrogram item to the given Cairo context|
||Conducts an inorder traversal of the merge tree.|
Creates a hierarchical clustering.
|merges||the merge history either in matrix or tuple format|
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.
Formats the dendrogram in a foreign format.
Currently only the Newick format is supported.
>>> d = Dendrogram([(2, 3), (0, 1), (4, 5)]) >>> d.format() '((2,3)4,(0,1)5)6;' >>> d.names = list("ABCDEFG") >>> d.format() '((C,D)E,(A,B)F)G;'
def names(self, items):
Sets the names of the nodes in the dendrogram
Returns the summary of the dendrogram.
The summary includes the number of leafs and branches, and also an ASCII art representation of the dendrogram unless it is too large.
|verbosity||determines whether the ASCII representation of the dendrogram should be printed. Zero verbosity prints only the number of leafs and branches.|
|max||the maximal number of leafs to print in the ASCII representation. If the dendrogram has more leafs than this limit, the ASCII representation will not be printed even if the verbosity is larger than or equal to 1.|
|the summary of the dendrogram as a string.|
def _convert_matrix_to_tuple_repr(merges, n=None):
Converts the matrix representation of a clustering to a tuple representation.
|merges||the matrix representation of the clustering|
|the tuple representation of the clustering|
Calculates the amount of space needed for drawing an individual vertex at the bottom of the dendrogram.
Plots a dendrogram item to the given Cairo context
|context||the Cairo context we are plotting on|
|horiz||whether the dendrogram is horizontally oriented|
|idx||the index of the item|
|x||the X position of the item|
|y||the Y position of the item|
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.
|the result of the inorder traversal in a list.|