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1 # -*- coding: utf-8 -*-
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2 """
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3 Created on Mon Jun 3 19:51:00 2019
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4 @author: Narger
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5 """
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6
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7 import sys
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8 import argparse
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9 import os
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10 import numpy as np
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11 import pandas as pd
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12 from sklearn.datasets import make_blobs
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13 from sklearn.cluster import KMeans, DBSCAN, AgglomerativeClustering
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14 from sklearn.metrics import silhouette_samples, silhouette_score, cluster
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15 import matplotlib
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16 matplotlib.use('agg')
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17 import matplotlib.pyplot as plt
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18 import scipy.cluster.hierarchy as shc
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19 import matplotlib.cm as cm
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20 from typing import Optional, Dict, List
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21
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22 ################################# process args ###############################
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155
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23 def process_args(args_in :List[str] = None) -> argparse.Namespace:
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24 """
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25 Processes command-line arguments.
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26
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27 Args:
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28 args (list): List of command-line arguments.
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29
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30 Returns:
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31 Namespace: An object containing parsed arguments.
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32 """
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33 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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34 description = 'process some value\'s' +
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35 ' genes to create class.')
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36
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37 parser.add_argument('-ol', '--out_log',
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38 help = "Output log")
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39
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40 parser.add_argument('-in', '--input',
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41 type = str,
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42 help = 'input dataset')
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43
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44 parser.add_argument('-cy', '--cluster_type',
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45 type = str,
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46 choices = ['kmeans', 'dbscan', 'hierarchy'],
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47 default = 'kmeans',
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48 help = 'choose clustering algorythm')
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49
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428
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50 parser.add_argument('-sc', '--scaling',
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51 type = str,
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52 choices = ['true', 'false'],
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53 default = 'true',
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54 help = 'choose if you want to scaling the data')
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55
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56 parser.add_argument('-k1', '--k_min',
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57 type = int,
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58 default = 2,
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59 help = 'choose minimun cluster number to be generated')
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60
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61 parser.add_argument('-k2', '--k_max',
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62 type = int,
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63 default = 7,
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64 help = 'choose maximum cluster number to be generated')
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65
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66 parser.add_argument('-el', '--elbow',
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67 type = str,
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317
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68 default = 'false',
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69 choices = ['true', 'false'],
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70 help = 'choose if you want to generate an elbow plot for kmeans')
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71
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72 parser.add_argument('-si', '--silhouette',
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73 type = str,
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317
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74 default = 'false',
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75 choices = ['true', 'false'],
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76 help = 'choose if you want silhouette plots')
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77
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78 parser.add_argument('-td', '--tool_dir',
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79 type = str,
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80 required = True,
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81 help = 'your tool directory')
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82
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83 parser.add_argument('-ms', '--min_samples',
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309
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84 type = int,
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85 help = 'min samples for dbscan (optional)')
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86
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87 parser.add_argument('-ep', '--eps',
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88 type = float,
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89 help = 'eps for dbscan (optional)')
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90
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91 parser.add_argument('-bc', '--best_cluster',
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92 type = str,
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93 help = 'output of best cluster tsv')
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94
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147
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95 parser.add_argument(
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96 '-idop', '--output_path',
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97 type = str,
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332
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98 default='clustering/',
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99 help = 'output path for maps')
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100
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101 args_in = parser.parse_args(args_in)
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102 return args_in
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103
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104 ########################### warning ###########################################
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105 def warning(s :str) -> None:
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106 """
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107 Log a warning message to an output log file and print it to the console.
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108
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109 Args:
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110 s (str): The warning message to be logged and printed.
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111
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112 Returns:
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113 None
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114 """
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309
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115
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116 with open(args.out_log, 'a') as log:
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117 log.write(s + "\n\n")
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118 print(s)
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119
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120 ########################## read dataset ######################################
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121 def read_dataset(dataset :str) -> pd.DataFrame:
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122 """
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123 Read dataset from a CSV file and return it as a Pandas DataFrame.
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124
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125 Args:
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126 dataset (str): the path to the dataset to convert into a DataFrame
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127
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128 Returns:
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129 pandas.DataFrame: The dataset loaded as a Pandas DataFrame.
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130
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131 Raises:
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132 pandas.errors.EmptyDataError: If the dataset file is empty.
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133 sys.exit: If the dataset file has the wrong format (e.g., fewer than 2 columns)
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134 """
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135 try:
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136 dataset = pd.read_csv(dataset, sep = '\t', header = 0)
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137 except pd.errors.EmptyDataError:
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138 sys.exit('Execution aborted: wrong format of dataset\n')
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139 if len(dataset.columns) < 2:
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140 sys.exit('Execution aborted: wrong format of dataset\n')
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141 return dataset
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142
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143 ############################ rewrite_input ###################################
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154
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144 def rewrite_input(dataset :Dict) -> Dict[str, List[Optional[float]]]:
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145 """
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146 Rewrite the dataset as a dictionary of lists instead of as a dictionary of dictionaries.
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147
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148 Args:
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149 dataset (pandas.DataFrame): The dataset to be rewritten.
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150
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151 Returns:
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152 dict: The rewritten dataset as a dictionary of lists.
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153 """
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154 #Riscrivo il dataset come dizionario di liste,
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155 #non come dizionario di dizionari
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153
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156 #dataset.pop('Reactions', None)
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157
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158 for key, val in dataset.items():
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159 l = []
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160 for i in val:
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161 if i == 'None':
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162 l.append(None)
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163 else:
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164 l.append(float(i))
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165
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166 dataset[key] = l
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167
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168 return dataset
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169
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170 ############################## write to csv ##################################
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171 def write_to_csv (dataset :pd.DataFrame, labels :List[str], name :str) -> None:
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172 """
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173 Write dataset and predicted labels to a CSV file.
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174
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175 Args:
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176 dataset (pandas.DataFrame): The dataset to be written.
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177 labels (list): The predicted labels for each data point.
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178 name (str): The name of the output CSV file.
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179
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180 Returns:
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181 None
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182 """
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183 #labels = predict
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184 predict = [x+1 for x in labels]
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185
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186 classe = (pd.DataFrame(list(zip(dataset.index, predict)))).astype(str)
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187
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188 dest = name
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189 classe.to_csv(dest, sep = '\t', index = False,
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190 header = ['Patient_ID', 'Class'])
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191
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192 ########################### trova il massimo in lista ########################
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193 def max_index (lista :List[int]) -> int:
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194 """
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195 Find the index of the maximum value in a list.
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196
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197 Args:
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198 lista (list): The list in which we search for the index of the maximum value.
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199
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200 Returns:
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201 int: The index of the maximum value in the list.
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202 """
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203 best = -1
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204 best_index = 0
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205 for i in range(len(lista)):
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206 if lista[i] > best:
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207 best = lista [i]
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208 best_index = i
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209
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210 return best_index
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211
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212 ################################ kmeans #####################################
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213 def kmeans (k_min: int, k_max: int, dataset: pd.DataFrame, elbow: str, silhouette: str, best_cluster: str) -> None:
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214 """
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215 Perform k-means clustering on the given dataset, which is an algorithm used to partition a dataset into groups (clusters) based on their characteristics.
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216 The goal is to divide the data into homogeneous groups, where the elements within each group are similar to each other and different from the elements in other groups.
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217
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218 Args:
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219 k_min (int): The minimum number of clusters to consider.
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220 k_max (int): The maximum number of clusters to consider.
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221 dataset (pandas.DataFrame): The dataset to perform clustering on.
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309
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222 elbow (str): Whether to generate an elbow plot for kmeans ('True' or 'False').
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223 silhouette (str): Whether to generate silhouette plots ('True' or 'False').
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224 best_cluster (str): The file path to save the output of the best cluster.
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225
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226 Returns:
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227 None
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228 """
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229 if not os.path.exists(args.output_path):
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230 os.makedirs(args.output_path)
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231
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232
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317
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233 if elbow == 'true':
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234 elbow = True
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235 else:
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236 elbow = False
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237
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317
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238 if silhouette == 'true':
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239 silhouette = True
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240 else:
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241 silhouette = False
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242
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243 range_n_clusters = [i for i in range(k_min, k_max+1)]
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244 distortions = []
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245 scores = []
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246 all_labels = []
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247
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248 clusterer = KMeans(n_clusters=1, random_state=10)
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249 distortions.append(clusterer.fit(dataset).inertia_)
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250
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251
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252 for n_clusters in range_n_clusters:
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253 clusterer = KMeans(n_clusters=n_clusters, random_state=10)
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254 cluster_labels = clusterer.fit_predict(dataset)
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255
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256 all_labels.append(cluster_labels)
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257 if n_clusters == 1:
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258 silhouette_avg = 0
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259 else:
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260 silhouette_avg = silhouette_score(dataset, cluster_labels)
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261 scores.append(silhouette_avg)
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262 distortions.append(clusterer.fit(dataset).inertia_)
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263
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264 best = max_index(scores) + k_min
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265
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266 for i in range(len(all_labels)):
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267 prefix = ''
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268 if (i + k_min == best):
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269 prefix = '_BEST'
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270
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271 write_to_csv(dataset, all_labels[i], f'{args.output_path}/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv')
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272
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273
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274 if (prefix == '_BEST'):
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275 labels = all_labels[i]
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276 predict = [x+1 for x in labels]
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277 classe = (pd.DataFrame(list(zip(dataset.index, predict)))).astype(str)
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278 classe.to_csv(best_cluster, sep = '\t', index = False, header = ['Patient_ID', 'Class'])
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279
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280
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281
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282
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283 if silhouette:
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284 silhouette_draw(dataset, all_labels[i], i + k_min, f'{args.output_path}/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png')
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285
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286
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287 if elbow:
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288 elbow_plot(distortions, k_min,k_max)
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289
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290
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291
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292
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293
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294 ############################## elbow_plot ####################################
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295 def elbow_plot (distortions: List[float], k_min: int, k_max: int) -> None:
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296 """
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297 Generate an elbow plot to visualize the distortion for different numbers of clusters.
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298 The elbow plot is a graphical tool used in clustering analysis to help identifying the appropriate number of clusters by looking for the point where the rate of decrease
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299 in distortion sharply decreases, indicating the optimal balance between model complexity and clustering quality.
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300
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301 Args:
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302 distortions (list): List of distortion values for different numbers of clusters.
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303 k_min (int): The minimum number of clusters considered.
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304 k_max (int): The maximum number of clusters considered.
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305
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306 Returns:
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307 None
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308 """
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309 plt.figure(0)
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310 x = list(range(k_min, k_max + 1))
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311 x.insert(0, 1)
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312 plt.plot(x, distortions, marker = 'o')
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313 plt.xlabel('Number of clusters (k)')
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314 plt.ylabel('Distortion')
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315 s = f'{args.output_path}/elbow_plot.png'
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316 fig = plt.gcf()
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317 fig.set_size_inches(18.5, 10.5, forward = True)
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318 fig.savefig(s, dpi=100)
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319
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320
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321 ############################## silhouette plot ###############################
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322 def silhouette_draw(dataset: pd.DataFrame, labels: List[str], n_clusters: int, path:str) -> None:
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323 """
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324 Generate a silhouette plot for the clustering results.
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325 The silhouette coefficient is a measure used to evaluate the quality of clusters obtained from a clustering algorithmand it quantifies how similar an object is to its own cluster compared to other clusters.
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326 The silhouette coefficient ranges from -1 to 1, where:
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327 - A value close to +1 indicates that the object is well matched to its own cluster and poorly matched to neighboring clusters. This implies that the object is in a dense, well-separated cluster.
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328 - A value close to 0 indicates that the object is close to the decision boundary between two neighboring clusters.
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329 - A value close to -1 indicates that the object may have been assigned to the wrong cluster.
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330
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331 Args:
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332 dataset (pandas.DataFrame): The dataset used for clustering.
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333 labels (list): The cluster labels assigned to each data point.
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334 n_clusters (int): The number of clusters.
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335 path (str): The path to save the silhouette plot image.
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336
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337 Returns:
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338 None
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339 """
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340 if n_clusters == 1:
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341 return None
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342
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343 silhouette_avg = silhouette_score(dataset, labels)
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344 warning("For n_clusters = " + str(n_clusters) +
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345 " The average silhouette_score is: " + str(silhouette_avg))
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346
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347 plt.close('all')
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348 # Create a subplot with 1 row and 2 columns
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349 fig, (ax1) = plt.subplots(1, 1)
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350
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351 fig.set_size_inches(18, 7)
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352
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353 # The 1st subplot is the silhouette plot
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354 # The silhouette coefficient can range from -1, 1 but in this example all
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355 # lie within [-0.1, 1]
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356 ax1.set_xlim([-1, 1])
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357 # The (n_clusters+1)*10 is for inserting blank space between silhouette
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358 # plots of individual clusters, to demarcate them clearly.
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359 ax1.set_ylim([0, len(dataset) + (n_clusters + 1) * 10])
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360
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361 # Compute the silhouette scores for each sample
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362 sample_silhouette_values = silhouette_samples(dataset, labels)
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363
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364 y_lower = 10
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365 for i in range(n_clusters):
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366 # Aggregate the silhouette scores for samples belonging to
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367 # cluster i, and sort them
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368 ith_cluster_silhouette_values = \
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369 sample_silhouette_values[labels == i]
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370
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371 ith_cluster_silhouette_values.sort()
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372
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373 size_cluster_i = ith_cluster_silhouette_values.shape[0]
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374 y_upper = y_lower + size_cluster_i
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375
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376 color = cm.nipy_spectral(float(i) / n_clusters)
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377 ax1.fill_betweenx(np.arange(y_lower, y_upper),
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378 0, ith_cluster_silhouette_values,
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379 facecolor=color, edgecolor=color, alpha=0.7)
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380
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381 # Label the silhouette plots with their cluster numbers at the middle
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382 ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
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383
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384 # Compute the new y_lower for next plot
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385 y_lower = y_upper + 10 # 10 for the 0 samples
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386
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387 ax1.set_title("The silhouette plot for the various clusters.")
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388 ax1.set_xlabel("The silhouette coefficient values")
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389 ax1.set_ylabel("Cluster label")
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390
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391 # The vertical line for average silhouette score of all the values
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392 ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
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393
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394 ax1.set_yticks([]) # Clear the yaxis labels / ticks
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395 ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
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396
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397
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398 plt.suptitle(("Silhouette analysis for clustering on sample data "
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399 "with n_clusters = " + str(n_clusters) + "\nAverage silhouette_score = " + str(silhouette_avg)), fontsize=12, fontweight='bold')
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400
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401
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402 plt.savefig(path, bbox_inches='tight')
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403
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404 ######################## dbscan ##############################################
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405 def dbscan(dataset: pd.DataFrame, eps: float, min_samples: float, best_cluster: str) -> None:
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406 """
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407 Perform DBSCAN clustering on the given dataset, which is a clustering algorithm that groups together closely packed points based on the notion of density.
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408
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409 Args:
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410 dataset (pandas.DataFrame): The dataset to be clustered.
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411 eps (float): The maximum distance between two samples for one to be considered as in the neighborhood of the other.
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412 min_samples (float): The number of samples in a neighborhood for a point to be considered as a core point.
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413 best_cluster (str): The file path to save the output of the best cluster.
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414
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415 Returns:
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416 None
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417 """
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147
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418 if not os.path.exists(args.output_path):
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419 os.makedirs(args.output_path)
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4
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420
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421 if eps is not None:
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422 clusterer = DBSCAN(eps = eps, min_samples = min_samples)
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423 else:
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424 clusterer = DBSCAN()
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425
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426 clustering = clusterer.fit(dataset)
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427
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428 core_samples_mask = np.zeros_like(clustering.labels_, dtype=bool)
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429 core_samples_mask[clustering.core_sample_indices_] = True
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430 labels = clustering.labels_
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431
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432 # Number of clusters in labels, ignoring noise if present.
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433 n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
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434
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435
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436 labels = labels
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437 predict = [x+1 for x in labels]
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438 classe = (pd.DataFrame(list(zip(dataset.index, predict)))).astype(str)
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439 classe.to_csv(best_cluster, sep = '\t', index = False, header = ['Patient_ID', 'Class'])
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440
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441
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442 ########################## hierachical #######################################
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443 def hierachical_agglomerative(dataset: pd.DataFrame, k_min: int, k_max: int, best_cluster: str, silhouette: str) -> None:
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444 """
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445 Perform hierarchical agglomerative clustering on the given dataset.
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446
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447 Args:
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448 dataset (pandas.DataFrame): The dataset to be clustered.
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449 k_min (int): The minimum number of clusters to consider.
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450 k_max (int): The maximum number of clusters to consider.
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451 best_cluster (str): The file path to save the output of the best cluster.
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309
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452 silhouette (str): Whether to generate silhouette plots ('True' or 'False').
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4
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453
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454 Returns:
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455 None
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456 """
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147
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457 if not os.path.exists(args.output_path):
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458 os.makedirs(args.output_path)
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4
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459
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460 plt.figure(figsize=(10, 7))
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461 plt.title("Customer Dendograms")
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462 shc.dendrogram(shc.linkage(dataset, method='ward'), labels=dataset.index.values.tolist())
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463 fig = plt.gcf()
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147
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464 fig.savefig(f'{args.output_path}/dendogram.png', dpi=200)
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4
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465
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466 range_n_clusters = [i for i in range(k_min, k_max+1)]
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467
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468 scores = []
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469 labels = []
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470
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471 n_classi = dataset.shape[0]
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472
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473 for n_clusters in range_n_clusters:
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474 cluster = AgglomerativeClustering(n_clusters=n_clusters, affinity='euclidean', linkage='ward')
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475 cluster.fit_predict(dataset)
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476 cluster_labels = cluster.labels_
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477 labels.append(cluster_labels)
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147
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478 write_to_csv(dataset, cluster_labels, f'{args.output_path}/hierarchical_with_' + str(n_clusters) + '_clusters.tsv')
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4
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479
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480 best = max_index(scores) + k_min
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481
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482 for i in range(len(labels)):
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483 prefix = ''
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484 if (i + k_min == best):
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485 prefix = '_BEST'
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317
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486 if silhouette == 'true':
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147
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487 silhouette_draw(dataset, labels[i], i + k_min, f'{args.output_path}/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png')
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4
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488
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489 for i in range(len(labels)):
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490 if (i + k_min == best):
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491 labels = labels[i]
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492 predict = [x+1 for x in labels]
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493 classe = (pd.DataFrame(list(zip(dataset.index, predict)))).astype(str)
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494 classe.to_csv(best_cluster, sep = '\t', index = False, header = ['Patient_ID', 'Class'])
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495
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496
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497 ############################# main ###########################################
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147
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498 def main(args_in:List[str] = None) -> None:
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4
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499 """
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500 Initializes everything and sets the program in motion based on the fronted input arguments.
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501
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502 Returns:
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503 None
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504 """
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147
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505 global args
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506 args = process_args(args_in)
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4
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507
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147
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508 if not os.path.exists(args.output_path):
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509 os.makedirs(args.output_path)
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444
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510
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4
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511 #Data read
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512
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513 X = read_dataset(args.input)
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154
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514 X = X.iloc[:, 1:]
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4
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515 X = pd.DataFrame.to_dict(X, orient='list')
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516 X = rewrite_input(X)
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517 X = pd.DataFrame.from_dict(X, orient = 'index')
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518
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519 for i in X.columns:
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224
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520 if any(val is None or np.isnan(val) for val in X[i]):
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4
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521 X = X.drop(columns=[i])
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522
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444
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523 if args.scaling == "true":
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428
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524 list_to_remove = []
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525 toll_std=1e-8
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526 for i in X.columns:
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527 mean_i = X[i].mean()
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528 std_i = X[i].std()
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529 if std_i >toll_std:
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530 #scaling with mean 0 and std 1
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531 X[i] = (X[i]-mean_i)/std_i
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532 else:
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533 #remove feature because std = 0 during clustering
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534 list_to_remove.append(i)
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535 if len(list_to_remove)>0:
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536 X = X.drop(columns=list_to_remove)
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537
|
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4
|
538 if args.k_max != None:
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539 numero_classi = X.shape[0]
|
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540 while args.k_max >= numero_classi:
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541 err = 'Skipping k = ' + str(args.k_max) + ' since it is >= number of classes of dataset'
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542 warning(err)
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543 args.k_max = args.k_max - 1
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544
|
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545
|
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546 if args.cluster_type == 'kmeans':
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547 kmeans(args.k_min, args.k_max, X, args.elbow, args.silhouette, args.best_cluster)
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548
|
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549 if args.cluster_type == 'dbscan':
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550 dbscan(X, args.eps, args.min_samples, args.best_cluster)
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551
|
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552 if args.cluster_type == 'hierarchy':
|
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553 hierachical_agglomerative(X, args.k_min, args.k_max, args.best_cluster, args.silhouette)
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554
|
|
|
555 ##############################################################################
|
|
|
556 if __name__ == "__main__":
|
|
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557 main()
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