geno4sd.utils.clustering_tools module

Summary

Functions:

eigenDecomposition	This method performs the eigen decomposition on a given affinity matrix
getAffinityMatrix	Calculate affinity matrix based on input coordinates matrix and the numeber of nearest neighbours.

Reference

getAffinityMatrix(coordinates, n_cluster=10)

Calculate affinity matrix based on input coordinates matrix and the numeber of nearest neighbours.

Apply local scaling based on the k nearest neighbour

References: https://papers.nips.cc/paper/2619-self-tuning-spectral-clustering.pdf

eigenDecomposition(A, plot=True, topK=5)

This method performs the eigen decomposition on a given affinity matrix

A:

Affinity matrix

plot:

plots the sorted eigen values for visual inspection

A tuple containing: - the optimal number of clusters by eigengap heuristic - all eigen values - all eigen vectors

References:

https://papers.nips.cc/paper/2619-self-tuning-spectral-clustering.pdf http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/Luxburg07_tutorial_4488%5b0%5d.pdf