tools.py

import numpy as np
from scipy.spatial.distance import squareform
from fastcluster import linkage
import umap

# ------------------------------------------------------------------------------------------------
#
#                                     Sim Matrix Ordering
#
# ------------------------------------------------------------------------------------------------

def seriation(Z,N,cur_index):
    '''
        input:
            - Z is a hierarchical tree (dendrogram)
            - N is the number of points given to the clustering process
            - cur_index is the position in the tree for the recursive traversal
        output:
            - order implied by the hierarchical tree Z
            
        seriation computes the order implied by a hierarchical tree (dendrogram)
    '''
    if cur_index < N:
        return [cur_index]
    else:
        left = int(Z[cur_index-N,0])
        right = int(Z[cur_index-N,1])
        return (seriation(Z,N,left) + seriation(Z,N,right))

def compute_serial_matrix(dist_mat,method="ward"):
    '''
        input:
            - dist_mat is a distance matrix
            - method = ["ward","single","average","complete"]
        output:
            - seriated_dist is the input dist_mat,
              but with re-ordered rows and columns
              according to the seriation, i.e. the
              order implied by the hierarchical tree
            - res_order is the order implied by
              the hierarhical tree
            - res_linkage is the hierarhical tree (dendrogram)
        
        compute_serial_matrix transforms a distance matrix into 
        a sorted distance matrix according to the order implied 
        by the hierarchical tree (dendrogram)
    '''
    N = len(dist_mat)
    flat_dist_mat = squareform(dist_mat)
    res_linkage = linkage(flat_dist_mat, method=method,preserve_input=True)
    res_order = seriation(res_linkage, N, N + N-2)
    seriated_dist = np.zeros((N,N))
    a,b = np.triu_indices(N,k=1)
    seriated_dist[a,b] = dist_mat[ [res_order[i] for i in a], [res_order[j] for j in b]]
    seriated_dist[b,a] = seriated_dist[a,b]
    
    return seriated_dist, res_order, res_linkage

def compute_ordered_matrix(sim_matrix,dist_matrix, model_names):
    if len(sim_matrix) >= 2:
        # Compute serial matrix (hierarchical clustering) for tab1
        ordered_dist_matrix, order, Z = compute_serial_matrix(dist_matrix)
        ordered_sim_matrix = sim_matrix[order][:, order]
        ordered_model_names = [model_names[i] for i in order]
    else:
        ordered_sim_matrix = sim_matrix
        ordered_model_names = model_names 

    return ordered_sim_matrix, ordered_model_names


# ------------------------------------------------------------------------------------------------
#
#                                     UMAP computation
#
# ------------------------------------------------------------------------------------------------

def compute_umap(dist_matrix,d=2):
    embedding = umap.UMAP(densmap=True,n_components=d, metric='precomputed',random_state=42).fit_transform(dist_matrix)
    return embedding