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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
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5 @author: Narger
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6 """
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7
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8 import sys
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9 import argparse
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10 import os
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11 from sklearn.datasets import make_blobs
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12 from sklearn.cluster import KMeans, DBSCAN, AgglomerativeClustering
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13 from sklearn.metrics import silhouette_samples, silhouette_score, davies_bouldin_score, cluster
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14 import matplotlib.pyplot as plt
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15 import scipy.cluster.hierarchy as shc
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16 import matplotlib.cm as cm
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17 import numpy as np
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18 import pandas as pd
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19
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16
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20 ################################# process args ###############################
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21
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22 def process_args(args):
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23 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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24 description = 'process some value\'s' +
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25 ' genes to create class.')
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26
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27 parser.add_argument('-ol', '--out_log',
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28 help = "Output log")
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29
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30 parser.add_argument('-in', '--input',
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31 type = str,
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32 help = 'input dataset')
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33
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34 parser.add_argument('-cy', '--cluster_type',
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35 type = str,
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36 choices = ['kmeans', 'meanshift', 'dbscan', 'hierarchy'],
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37 default = 'kmeans',
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38 help = 'choose clustering algorythm')
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39
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40 parser.add_argument('-k1', '--k_min',
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41 type = int,
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42 default = 2,
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43 help = 'choose minimun cluster number to be generated')
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44
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45 parser.add_argument('-k2', '--k_max',
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46 type = int,
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47 default = 7,
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48 help = 'choose maximum cluster number to be generated')
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49
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50 parser.add_argument('-el', '--elbow',
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51 type = str,
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52 default = 'false',
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53 choices = ['true', 'false'],
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54 help = 'choose if you want to generate an elbow plot for kmeans')
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55
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56 parser.add_argument('-si', '--silhouette',
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57 type = str,
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58 default = 'false',
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59 choices = ['true', 'false'],
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60 help = 'choose if you want silhouette plots')
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61
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62 parser.add_argument('-db', '--davies',
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63 type = str,
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64 default = 'false',
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65 choices = ['true', 'false'],
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66 help = 'choose if you want davies bouldin scores')
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67
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68 parser.add_argument('-td', '--tool_dir',
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69 type = str,
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70 required = True,
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71 help = 'your tool directory')
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72
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73 parser.add_argument('-ms', '--min_samples',
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74 type = int,
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75 help = 'min samples for dbscan (optional)')
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76
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77 parser.add_argument('-ep', '--eps',
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78 type = int,
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79 help = 'eps for dbscan (optional)')
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80
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81
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82 args = parser.parse_args()
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83 return args
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84
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85 ########################### warning ###########################################
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86
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87 def warning(s):
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88 args = process_args(sys.argv)
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89 with open(args.out_log, 'a') as log:
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90 log.write(s + "\n\n")
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91 print(s)
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92
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93 ########################## read dataset ######################################
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94
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95 def read_dataset(dataset):
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96 try:
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97 dataset = pd.read_csv(dataset, sep = '\t', header = 0)
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98 except pd.errors.EmptyDataError:
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99 sys.exit('Execution aborted: wrong format of dataset\n')
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100 if len(dataset.columns) < 2:
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101 sys.exit('Execution aborted: wrong format of dataset\n')
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102 return dataset
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103
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104 ############################ rewrite_input ###################################
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105
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106 def rewrite_input(dataset):
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107 #Riscrivo il dataset come dizionario di liste,
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108 #non come dizionario di dizionari
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109
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110 for key, val in dataset.items():
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111 l = []
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112 for i in val:
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113 if i == 'None':
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114 l.append(None)
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115 else:
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116 l.append(float(i))
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117
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118 dataset[key] = l
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119
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120 return dataset
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121
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122 ############################## write to csv ##################################
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123
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124 def write_to_csv (dataset, labels, name):
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125 list_labels = labels
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126 list_values = dataset
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127
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128 list_values = list_values.tolist()
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129 d = {'Label' : list_labels, 'Value' : list_values}
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130
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131 df = pd.DataFrame(d, columns=['Value','Label'])
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132
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133 dest = name + '.tsv'
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134 df.to_csv(dest, sep = '\t', index = False,
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135 header = ['Value', 'Label'])
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136
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137 ########################### trova il massimo in lista ########################
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138 def max_index (lista):
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139 best = -1
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140 best_index = 0
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141 for i in range(len(lista)):
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142 if lista[i] > best:
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143 best = lista [i]
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144 best_index = i
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145
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146 return best_index
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147
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148 ################################ kmeans #####################################
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149
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150 def kmeans (k_min, k_max, dataset, elbow, silhouette, davies):
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151 if not os.path.exists('clustering/kmeans_output'):
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152 os.makedirs('clustering/kmeans_output')
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153
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154
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155 if elbow == 'true':
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156 elbow = True
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157 else:
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158 elbow = False
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159
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160 if silhouette == 'true':
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161 silhouette = True
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162 else:
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163 silhouette = False
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164
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165 if davies == 'true':
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166 davies = True
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167 else:
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168 davies = False
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169
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170
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171 range_n_clusters = [i for i in range(k_min, k_max+1)]
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172 distortions = []
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173 scores = []
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174 all_labels = []
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175
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176 for n_clusters in range_n_clusters:
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177 clusterer = KMeans(n_clusters=n_clusters, random_state=10)
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178 cluster_labels = clusterer.fit_predict(dataset)
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179
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180 all_labels.append(cluster_labels)
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181 silhouette_avg = silhouette_score(dataset, cluster_labels)
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182 scores.append(silhouette_avg)
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183 distortions.append(clusterer.fit(dataset).inertia_)
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184
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185 best = max_index(scores) + k_min
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186
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187 for i in range(len(all_labels)):
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188 prefix = ''
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189 if (i + k_min == best):
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190 prefix = '_BEST'
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191
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192 write_to_csv(dataset, all_labels[i], 'clustering/kmeans_output/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv')
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193
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194 if davies:
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195 with np.errstate(divide='ignore', invalid='ignore'):
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196 davies_bouldin = davies_bouldin_score(dataset, all_labels[i])
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197 warning("\nFor n_clusters = " + str(i + k_min) +
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198 " The average davies bouldin score is: " + str(davies_bouldin))
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199
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200
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201 if silhouette:
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202 silihouette_draw(dataset, all_labels[i], i + k_min, 'clustering/kmeans_output/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png')
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203
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204
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205 if elbow:
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206 elbow_plot(distortions, k_min,k_max)
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207
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208
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209
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210
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211
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212 ############################## elbow_plot ####################################
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213
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214 def elbow_plot (distortions, k_min, k_max):
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215 plt.figure(0)
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216 plt.plot(range(k_min, k_max+1), distortions, marker = 'o')
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217 plt.xlabel('Number of cluster')
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218 plt.ylabel('Distortion')
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219 s = 'clustering/kmeans_output/elbow_plot.png'
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220 fig = plt.gcf()
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221 fig.set_size_inches(18.5, 10.5, forward = True)
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222 fig.savefig(s, dpi=100)
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223
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224
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225 ############################## silhouette plot ###############################
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226 def silihouette_draw(dataset, labels, n_clusters, path):
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227 silhouette_avg = silhouette_score(dataset, labels)
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228 warning("For n_clusters = " + str(n_clusters) +
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229 " The average silhouette_score is: " + str(silhouette_avg))
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230
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231 plt.close('all')
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232 # Create a subplot with 1 row and 2 columns
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233 fig, (ax1) = plt.subplots(1, 1)
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234
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235 fig.set_size_inches(18, 7)
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236
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237 # The 1st subplot is the silhouette plot
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238 # The silhouette coefficient can range from -1, 1 but in this example all
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239 # lie within [-0.1, 1]
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240 ax1.set_xlim([-1, 1])
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241 # The (n_clusters+1)*10 is for inserting blank space between silhouette
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242 # plots of individual clusters, to demarcate them clearly.
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243 ax1.set_ylim([0, len(dataset) + (n_clusters + 1) * 10])
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244
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245 # Compute the silhouette scores for each sample
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246 sample_silhouette_values = silhouette_samples(dataset, labels)
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247
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248 y_lower = 10
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249 for i in range(n_clusters):
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250 # Aggregate the silhouette scores for samples belonging to
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251 # cluster i, and sort them
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252 ith_cluster_silhouette_values = \
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253 sample_silhouette_values[labels == i]
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254
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255 ith_cluster_silhouette_values.sort()
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256
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257 size_cluster_i = ith_cluster_silhouette_values.shape[0]
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258 y_upper = y_lower + size_cluster_i
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259
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260 color = cm.nipy_spectral(float(i) / n_clusters)
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261 ax1.fill_betweenx(np.arange(y_lower, y_upper),
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262 0, ith_cluster_silhouette_values,
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263 facecolor=color, edgecolor=color, alpha=0.7)
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264
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265 # Label the silhouette plots with their cluster numbers at the middle
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266 ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
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267
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268 # Compute the new y_lower for next plot
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269 y_lower = y_upper + 10 # 10 for the 0 samples
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270
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271 ax1.set_title("The silhouette plot for the various clusters.")
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272 ax1.set_xlabel("The silhouette coefficient values")
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273 ax1.set_ylabel("Cluster label")
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274
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275 # The vertical line for average silhouette score of all the values
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276 ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
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277
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278 ax1.set_yticks([]) # Clear the yaxis labels / ticks
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279 ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
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280
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281
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282 plt.suptitle(("Silhouette analysis for clustering on sample data "
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283 "with n_clusters = " + str(n_clusters) + "\nAverage silhouette_score = " + str(silhouette_avg)), fontsize=12, fontweight='bold')
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284
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285
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286 plt.savefig(path, bbox_inches='tight')
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287
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288 ######################## dbscan ##############################################
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289
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290 def dbscan(dataset, eps, min_samples):
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291 if not os.path.exists('clustering/dbscan_output'):
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292 os.makedirs('clustering/dbscan_output')
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293
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294 if eps is not None:
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295 clusterer = DBSCAN(eps = eps, min_samples = min_samples)
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296 else:
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297 clusterer = DBSCAN()
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298
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299 clustering = clusterer.fit(dataset)
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300
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301 core_samples_mask = np.zeros_like(clustering.labels_, dtype=bool)
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302 core_samples_mask[clustering.core_sample_indices_] = True
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303 labels = clustering.labels_
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304
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305 # Number of clusters in labels, ignoring noise if present.
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306 n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
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307
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308 silhouette_avg = silhouette_score(dataset, labels)
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309 warning("For n_clusters =" + str(n_clusters_) +
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310 "The average silhouette_score is :" + str(silhouette_avg))
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311
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312 ##TODO: PLOT SU DBSCAN (no centers) e HIERARCHICAL
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313
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314 # Black removed and is used for noise instead.
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315 unique_labels = set(labels)
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316 colors = [plt.cm.Spectral(each)
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317 for each in np.linspace(0, 1, len(unique_labels))]
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318 for k, col in zip(unique_labels, colors):
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319 if k == -1:
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320 # Black used for noise.
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321 col = [0, 0, 0, 1]
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322
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323 class_member_mask = (labels == k)
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324
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325 xy = dataset[class_member_mask & core_samples_mask]
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326 plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col),
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327 markeredgecolor='k', markersize=14)
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328
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329 xy = dataset[class_member_mask & ~core_samples_mask]
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330 plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col),
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331 markeredgecolor='k', markersize=6)
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332
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333 plt.title('Estimated number of clusters: %d' % n_clusters_)
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334 s = 'clustering/dbscan_output/dbscan_plot.png'
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335 fig = plt.gcf()
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336 fig.set_size_inches(18.5, 10.5, forward = True)
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337 fig.savefig(s, dpi=100)
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338
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339
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340 write_to_csv(dataset, labels, 'clustering/dbscan_output/dbscan_results.tsv')
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341
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342 ########################## hierachical #######################################
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343
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344 def hierachical_agglomerative(dataset, k_min, k_max):
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345
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346 if not os.path.exists('clustering/agglomerative_output'):
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347 os.makedirs('clustering/agglomerative_output')
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348
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349 plt.figure(figsize=(10, 7))
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350 plt.title("Customer Dendograms")
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351 shc.dendrogram(shc.linkage(dataset, method='ward'))
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352 fig = plt.gcf()
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353 fig.savefig('clustering/agglomerative_output/dendogram.png', dpi=200)
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354
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355 range_n_clusters = [i for i in range(k_min, k_max+1)]
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356
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357 for n_clusters in range_n_clusters:
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358
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359 cluster = AgglomerativeClustering(n_clusters=n_clusters, affinity='euclidean', linkage='ward')
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360 cluster.fit_predict(dataset)
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361 cluster_labels = cluster.labels_
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362
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363 silhouette_avg = silhouette_score(dataset, cluster_labels)
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364 warning("For n_clusters =", n_clusters,
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365 "The average silhouette_score is :", silhouette_avg)
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366
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367 plt.clf()
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368 plt.figure(figsize=(10, 7))
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369 plt.title("Agglomerative Hierarchical Clustering\nwith " + str(n_clusters) + " clusters and " + str(silhouette_avg) + " silhouette score")
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370 plt.scatter(dataset[:,0], dataset[:,1], c = cluster_labels, cmap='rainbow')
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371 s = 'clustering/agglomerative_output/hierachical_' + str(n_clusters) + '_clusters.png'
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372 fig = plt.gcf()
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373 fig.set_size_inches(10, 7, forward = True)
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374 fig.savefig(s, dpi=200)
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375
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376 write_to_csv(dataset, cluster_labels, 'clustering/agglomerative_output/agglomerative_hierarchical_with_' + str(n_clusters) + '_clusters.tsv')
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377
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378
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379
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380
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381 ############################# main ###########################################
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382
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383
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384 def main():
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16
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385 if not os.path.exists('clustering'):
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386 os.makedirs('clustering')
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387
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0
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388 args = process_args(sys.argv)
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16
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389
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390 #Data read
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391
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392 X = read_dataset(args.input)
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393 X = pd.DataFrame.to_dict(X, orient='list')
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394 X = rewrite_input(X)
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395 X = pd.DataFrame.from_dict(X, orient = 'index')
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396
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397 for i in X.columns:
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398 tmp = X[i][0]
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399 if tmp == None:
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400 X = X.drop(columns=[i])
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401
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402 X = pd.DataFrame.to_numpy(X)
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403
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404
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405 if args.cluster_type == 'kmeans':
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406 kmeans(args.k_min, args.k_max, X, args.elbow, args.silhouette, args.davies)
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407
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408 if args.cluster_type == 'dbscan':
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409 dbscan(X, args.eps, args.min_samples)
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410
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411 if args.cluster_type == 'hierarchy':
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412 hierachical_agglomerative(X, args.k_min, args.k_max)
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413
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414 ##############################################################################
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0
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415
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416 if __name__ == "__main__":
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6
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417 main()
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