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1 import itertools
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2 import pandas as pd
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3 from math import pi
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4 import numpy as np
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5 import matplotlib.pyplot as plt
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6 import math
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7 import logomaker as lm
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8 from fpdf import FPDF, fpdf
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9 import glob
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10
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11 #################################################################################################################################################################
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12
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13 def pie_non_temp(merge_con,merge_non_con,merge_tre,merge_non_tre,c_unmap,t_unmap,c_unmap_counts,t_unmap_counts,group_name1,group_name2):
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14
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15 c_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_con]
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16 t_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_tre]
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17 c_non_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_non_con]
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18 t_non_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_non_tre]
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19
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20 c_templ = 0
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21 c_tem_counts = 0
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22 c_mature = 0
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23 c_mat_counts = 0
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24 t_templ = 0
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25 t_tem_counts = 0
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26 t_mature = 0
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27 t_mat_counts = 0
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28
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29 c_non = len(c_non_samples)
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30 c_non_counts = sum(x[2] for x in c_non_samples)
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31 t_non = len(t_non_samples)
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32 t_non_counts = sum(x[2] for x in t_non_samples)
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33
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34 c_unmap = c_unmap - c_non
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35 t_unmap = c_unmap - t_non
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36
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37 c_unmap_counts=c_unmap_counts - c_non_counts
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38 t_unmap_counts=t_unmap_counts - t_non_counts
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39
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40
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41 for x in c_samples:
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42
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43 if "/" not in x[0]:
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44 if "chr" in x[0].split("_")[-1]:
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45 c_mature+=1
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46 c_mat_counts += x[2]
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47 else:
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48 c_templ+=1
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49 c_tem_counts += x[2]
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50 else:
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51 f=0
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52 for y in x[0].split("/"):
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53 if "chr" in y.split("_")[-1]:
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54 c_mature+=1
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55 c_mat_counts += x[2]
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56 f=1
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57 break
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58 if f==0:
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59 c_templ+=1
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60 c_tem_counts += x[2]
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61
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62 for x in t_samples:
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63
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64 if "/" not in x[0]:
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65 if "chr" in x[0].split("_")[-1]:
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66 t_mature+=1
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67 t_mat_counts += x[2]
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68 else:
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69 t_templ+=1
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70 t_tem_counts += x[2]
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71 else:
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72 f=0
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73 for y in x[0].split("/"):
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74 if "chr" in y.split("_")[-1]:
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75 t_mature+=1
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76 t_mat_counts += x[2]
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77 f=1
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78 break
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79 if f==0:
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80 t_templ+=1
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81 t_tem_counts += x[2]
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82
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83 fig = plt.figure(figsize=(7,5))
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84 labels = 'miRNA RefSeq','templated', 'unassigned','non-templated'
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85 sizes = [c_mat_counts, c_tem_counts, c_unmap_counts,c_non_counts]
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86 colors = ['gold', 'yellowgreen', 'lightcoral', 'lightskyblue']
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87 ax1 = plt.subplot2grid((1,2),(0,0))
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88 patches, texts, autotexts=plt.pie(sizes, labels=labels, colors=colors, startangle=140,autopct='%1.1f%%',radius=0.8)
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89 [x.set_fontsize(10) for x in texts]
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90 plt.title(group_name1.capitalize() + ' group (reads)',fontsize=12)
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91 labels = 'miRNA RefSeq','templated', 'unassigned','non-templated'
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92 sizes = [t_mat_counts, t_tem_counts, t_unmap_counts, t_non_counts]
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93 colors = ['gold', 'yellowgreen', 'lightcoral', 'lightskyblue']
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94 ax2 = plt.subplot2grid((1,2),(0,1))
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95 patches, texts, autotexts=plt.pie(sizes, labels=labels, colors=colors, startangle=140,autopct='%1.1f%%',radius=0.8)
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96 [x.set_fontsize(10) for x in texts]
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97 plt.title(group_name2.capitalize() + ' group (reads)', fontsize=12)
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98 plt.savefig('pie_non.png',dpi=300)
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99
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100 ######################################################################################################################################################
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101
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102
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103 def pie_temp(merge_con,c_unmap,c_unmap_counts,merge_tre,t_unmap,t_unmap_counts,group_name1,group_name2):
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104
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105 c_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_con]
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106 t_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_tre]
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107
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108 c_templ = 0
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109 c_tem_counts = 0
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110 c_mature = 0
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111 c_mat_counts = 0
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112 t_templ = 0
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113 t_tem_counts = 0
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114 t_mature = 0
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115 t_mat_counts = 0
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116
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117 for x in c_samples:
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118
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119 if "/" not in x[0]:
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120 if "chr" in x[0].split("_")[-1]:
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121 c_mature+=1
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122 c_mat_counts += x[2]
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123 else:
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124 c_templ+=1
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125 c_tem_counts += x[2]
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126 else:
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127 f=0
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128 for y in x[0].split("/"):
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129 if "chr" in y.split("_")[-1]:
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130 c_mature+=1
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131 c_mat_counts += x[2]
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132 f=1
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133 break
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134 if f==0:
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135 c_templ+=1
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136 c_tem_counts += x[2]
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137
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138 for x in t_samples:
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139
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140 if "/" not in x[0]:
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141 if "chr" in x[0].split("_")[-1]:
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142 t_mature+=1
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143 t_mat_counts += x[2]
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144 else:
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145 t_templ+=1
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146 t_tem_counts += x[2]
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147 else:
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148 f=0
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149 for y in x[0].split("/"):
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150 if "chr" in y.split("_")[-1]:
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151 t_mature+=1
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152 t_mat_counts += x[2]
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153 f=1
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154 break
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155 if f==0:
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156 t_templ+=1
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157 t_tem_counts += x[2]
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158
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159
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160 fig = plt.figure()
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19
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161 labels = 'miRNA RefSeq','templated', 'unassigned'
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3
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162 sizes = [c_mat_counts, c_tem_counts, c_unmap_counts]
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163 colors = ['gold', 'yellowgreen', 'lightskyblue']
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164 explode = (0.2, 0.05, 0.1)
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165 ax1 = plt.subplot2grid((1,2),(0,0))
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166 patches, texts, autotexts=plt.pie(sizes, labels=labels, colors=colors, startangle=140,autopct='%1.1f%%',radius=0.8)
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167 [x.set_fontsize(10) for x in texts]
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168 plt.title(group_name1.capitalize() + ' group (reads)', fontsize=12)
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169 labels = 'miRNA RefSeq','templated', 'unassigned'
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170 sizes = [t_mat_counts, t_tem_counts, t_unmap_counts]
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171 colors = ['gold', 'yellowgreen', 'lightskyblue']
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172 explode = (0.2, 0.05, 0.1)
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173 ax2 = plt.subplot2grid((1,2),(0,1))
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174 patches, texts, autotexts=plt.pie(sizes, labels=labels, colors=colors, startangle=140,autopct='%1.1f%%',radius=0.8)
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175 [x.set_fontsize(10) for x in texts]
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176 plt.title(group_name2.capitalize() + ' group (reads)',fontsize = 12)
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177 plt.savefig('pie_tem.png',dpi=300)
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178
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179 ###################################################################################################################################################################################################################
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180
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181
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182 def make_spider(merge_con,merge_tre,group_name1,group_name2):
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183
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184 c_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_con]
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185 t_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge_tre]
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186
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187 c_5 = 0
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188 c_5_counts = 0
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189 c_3 = 0
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190 c_3_counts = 0
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191 c_both =0
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192 c_both_counts=0
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193 c_mature = 0
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194 c_mat_counts = 0
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195 c_exception=0
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196 c_exception_counts=0
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197
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198
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199 t_5 = 0
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200 t_5_counts = 0
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201 t_3 = 0
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202 t_3_counts = 0
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203 t_both = 0
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204 t_both_counts = 0
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205 t_mature = 0
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206 t_mat_counts = 0
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207 t_exception = 0
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208 t_exception_counts=0
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209
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210 for x in c_samples:
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211
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212 if "/" not in x[0]:
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213 if "chr" in x[0].split("_")[-1]:
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214 c_mature+=1
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215 c_mat_counts += x[2]
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216 elif 0 == int(x[0].split("_")[-1]):
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217 c_5+=1
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218 c_5_counts += x[2]
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219 elif 0 == int(x[0].split("_")[-2]):
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220 c_3+=1
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221 c_3_counts += x[2]
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222 else:
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223 c_both+=1
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224 c_both_counts+=x[2]
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225
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226 else:
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227 f=0
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228 for y in x[0].split("/"):
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229 if "chr" in y.split("_")[-1]:
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230 c_mature+=1
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231 c_mat_counts += x[2]
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232 f=1
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233 break
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234 if f==0:
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235 for y in x[0].split("/"):
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236 c_exception+=1
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237 c_exception_counts += x[2]
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238
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239
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240 for x in t_samples:
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241
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242 if "/" not in x[0]:
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243 if "chr" in x[0].split("_")[-1]:
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244 t_mature+=1
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245 t_mat_counts += x[2]
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246 elif 0 == int(x[0].split("_")[-1]):
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247 t_5+=1
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248 t_5_counts += x[2]
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249 elif 0 == int(x[0].split("_")[-2]):
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250 t_3+=1
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251 t_3_counts += x[2]
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252 else:
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253 t_both+=1
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254 t_both_counts+=x[2]
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255
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256 else:
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257 f=0
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258 for y in x[0].split("/"):
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259 if "chr" in y.split("_")[-1]:
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260 t_mature+=1
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261 t_mat_counts += x[2]
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262 f=1
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263 break
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264 if f==0:
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265 for y in x[0].split("/"):
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266 t_exception+=1
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267 t_exception_counts += x[2]
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268
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269
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270 c_all = c_5+c_3+c_both+c_mature+c_exception
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271 c_all_counts = c_5_counts + c_3_counts + c_both_counts + c_mat_counts + c_exception_counts
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272
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273 t_all = t_5+t_3+t_both+t_mature + t_exception
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274 t_all_counts = t_5_counts + t_3_counts + t_both_counts + t_mat_counts + t_exception_counts
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275
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276 c_5 = round(c_5/c_all*100,2)
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277 c_3 = round(c_3/c_all*100,2)
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278 c_both = round(c_both/c_all*100,2)
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279 c_mature = round(c_mature/c_all*100,2)
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280 c_exception = round(c_exception/c_all*100,2)
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281
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282 c_5_counts = round(c_5_counts/c_all_counts*100,2)
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283 c_3_counts = round(c_3_counts/c_all_counts*100,2)
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284 c_both_counts = round(c_both_counts/c_all_counts*100,2)
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285 c_mat_counts = round(c_mat_counts/c_all_counts*100,2)
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286 c_exception_counts = round(c_exception_counts/c_all_counts*100,2)
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287
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288 t_5 = round(t_5/t_all*100,2)
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289 t_3 = round(t_3/t_all*100,2)
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290 t_both = round(t_both/t_all*100,2)
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291 t_mature = round(t_mature/t_all*100,2)
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292 t_exception = round(t_exception/t_all*100,2)
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293
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294 t_5_counts = round(t_5_counts/t_all_counts*100,2)
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295 t_3_counts = round(t_3_counts/t_all_counts*100,2)
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296 t_both_counts = round(t_both_counts/t_all_counts*100,2)
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297 t_mat_counts = round(t_mat_counts/t_all_counts*100,2)
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298 t_exception_counts = round(t_exception_counts/t_all_counts*100,2)
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299
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300 radar_max = max(c_5, c_3, c_both,c_mature,c_exception,t_5,t_3,t_both,t_mature,t_exception)
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301 radar_max_counts = max(c_5_counts,c_3_counts,c_both_counts,c_mat_counts,c_exception_counts,t_5_counts,t_3_counts,t_both_counts,t_mat_counts,t_exception_counts)
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302
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303 df=pd.DataFrame({
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304 'group':[group_name1.capitalize(),group_name2.capitalize()],
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3
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305 """5'3'-isomiRs""":[c_both,t_both],
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306 """3'-isomiRs""":[c_3,t_3],
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307 'RefSeq miRNA':[c_mature,t_mature],
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308 """5'-isomiRs""":[c_5,t_5],
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309 'others*':[c_exception,t_exception]})
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3
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310
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311 df1=pd.DataFrame({
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312 'group':[group_name1.capitalize(),group_name2.capitalize()],
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313 """5'3'-isomiRs""":[c_both_counts,t_both_counts],
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314 """3'-isomiRs""":[c_3_counts,t_3_counts],
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315 'RefSeq miRNA':[c_mat_counts,t_mat_counts],
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316 """5'-isomiRs""":[c_5_counts,t_5_counts],
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317 'others*':[c_exception_counts,t_exception_counts]})
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3
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318
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319 spider_last(df,radar_max,1,group_name1,group_name2)
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320 spider_last(df1,radar_max_counts,2,group_name1,group_name2)
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321
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322 #####################################################################################################################################################
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323
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324 def spider_last(df,radar_max,flag,group_name1,group_name2):
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325 # ------- PART 1: Create background
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326 fig = plt.figure()
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327 # number of variable
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328 categories=list(df)[1:]
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329 N = len(categories)
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330
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331 # What will be the angle of each axis in the plot? (we divide the plot / number of variable)
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332 angles = [n / float(N) * 2 * pi for n in range(N)]
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333 angles += angles[:1]
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334
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335 # Initialise the spider plot
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336 ax = plt.subplot(111, polar=True)
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337
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338 # If you want the first axis to be on top:
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339 ax.set_theta_offset(pi/2)
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340 ax.set_theta_direction(-1)
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341
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342 # Draw one axe per variable + add labels labels yet
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343 plt.xticks(angles[:-1], categories, fontsize=13)
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3
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344
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345 # Draw ylabels
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346 radar_max=round(radar_max+radar_max*0.1)
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347 mul=len(str(radar_max))-1
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348 maxi=int(math.ceil(radar_max / pow(10,mul))) * pow(10,mul)
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349 sep = round(maxi/4)
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16
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350 plt.yticks([sep, 2*sep, 3*sep, 4*sep, 5*sep], [str(sep)+'%', str(2*sep)+'%', str(3*sep)+'%', str(4*sep)+'%', str(5*sep)+'%'], color="grey", size=12)
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3
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351 plt.ylim(0, maxi)
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352
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353 # ------- PART 2: Add plots
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354
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355 # Plot each individual = each line of the data
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16
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356 # I don't do a loop, because plotting more than 2 groups makes the chart unreadable
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3
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357
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358 # Ind1
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359 values=df.loc[0].drop('group').values.flatten().tolist()
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360 values += values[:1]
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16
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361 ax.plot(angles, values,'-o', linewidth=1, linestyle='solid', label=group_name1.capitalize())
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3
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362 ax.fill(angles, values, 'b', alpha=0.1)
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363
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364 # Ind2
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365 values=df.loc[1].drop('group').values.flatten().tolist()
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366 values += values[:1]
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16
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367 ax.plot(angles, values, '-o' ,linewidth=1, linestyle='solid', label=group_name2.capitalize())
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3
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368 ax.fill(angles, values, 'r', alpha=0.1)
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369
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370 # Add legend
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371 if flag==1:
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16
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372 plt.legend(loc='upper right', prop={'size': 11}, bbox_to_anchor=(0.0, 0.1))
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3
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373 plt.savefig('spider_non_red.png',dpi=300)
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374 else:
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16
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375 plt.legend(loc='upper right', prop={'size': 11}, bbox_to_anchor=(0.0, 0.1))
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3
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376 plt.savefig('spider_red.png',dpi=300)
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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 def hist_red(samples,flag,group_name):
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382
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383 lengths=[]
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384 cat=[]
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385 total_reads=0
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386 seq=[]
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387
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388 if flag == "c":
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16
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389 title = "Length distribution of "+ group_name.lower() +" group (redundant reads)"
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3
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390 if flag == "t":
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16
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391 title = "Length distribution of "+ group_name.lower() +" group (redundant reads)"
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3
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392
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393 # classification of the sequences on two categories mapped or unmapped
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394 for i in samples:
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395 for x in i:
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396 lengths.append(x[3])
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397 if x[1]=="0":
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398 seq.append([x[3],x[0].split("-")[1],"Mapped"])
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399 cat.append("Mapped")
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400 if x[1] == "4":
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401 seq.append([x[3],x[0].split("-")[1],"Unassigned"])
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402 cat.append("Unassigned")
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403
|
|
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404 # Keep lengths below 35nts
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405 uni_len=list(set(lengths))
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406 uni_len=[x for x in uni_len if x<=35]
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407
|
|
|
408 # Remove duplicates from sequences
|
|
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409 seq.sort()
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|
|
410 uni_seq=list(seq for seq,_ in itertools.groupby(seq))
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411
|
|
|
412 # Calculation of the reads per group (mapped or unmapped)
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|
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413 total_reads+=sum([int(x[1]) for x in uni_seq])
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|
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414 map_reads=[]
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|
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415 unmap_reads=[]
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|
|
416 length=[]
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|
|
417 for y in uni_len:
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|
|
418 map_temp=0
|
|
|
419 unmap_temp=0
|
|
|
420 for x in uni_seq:
|
|
|
421 if x[0]==y and x[2]=="Mapped":
|
|
|
422 map_temp+=int(x[1])
|
|
|
423 if x[0]==y and x[2]=="Unassigned":
|
|
|
424 unmap_temp+=int(x[1])
|
|
|
425 length.append(y)
|
|
|
426 map_reads.append(round(map_temp/total_reads*100,2)) # percentage of mapped reads over total number of sequences
|
|
|
427 unmap_reads.append(round(unmap_temp/total_reads*100,2)) # percentage of unmapped reads over total number of sequences
|
|
|
428
|
|
|
429 # Generation of the graph
|
|
|
430 ylim=max([sum(x) for x in zip(unmap_reads, map_reads)])
|
|
|
431 ylim=ylim+ylim*20/100
|
|
|
432 fig, ax = plt.subplots()
|
|
|
433 width=0.8
|
|
|
434 ax.bar(length, unmap_reads, width, label='Unassigned')
|
|
|
435 h=ax.bar(length, map_reads, width, bottom=unmap_reads, label='Mapped')
|
|
|
436 plt.xticks(np.arange(length[0], length[-1]+1, 1))
|
|
|
437 plt.yticks(np.arange(0, ylim, 5))
|
|
|
438 plt.xlabel('Length (nt)',fontsize=14)
|
|
|
439 plt.ylabel('Percentage',fontsize=14)
|
|
|
440 plt.title(title,fontsize=14)
|
|
|
441 ax.legend()
|
|
|
442 plt.ylim([0, ylim])
|
|
|
443 ax.grid(axis='y',linewidth=0.2)
|
|
|
444
|
|
|
445 # Save of the graph
|
|
|
446 if flag=='c':
|
|
|
447 plt.savefig('c_hist_red.png',dpi=300)
|
|
|
448
|
|
|
449 if flag=='t':
|
|
|
450 plt.savefig('t_hist_red.png',dpi=300)
|
|
|
451
|
|
|
452 #################################################################################################################
|
|
|
453
|
|
|
454 def logo_seq_red(merge, flag, group_name):
|
|
|
455
|
|
|
456 if flag=="c":
|
|
19
|
457 titlos= group_name.capitalize() + " group (redundant)"
|
|
3
|
458 file_logo="c_logo.png"
|
|
|
459 file_bar="c_bar.png"
|
|
|
460 if flag=="t":
|
|
19
|
461 titlos= group_name.capitalize() + " group (redundant)"
|
|
3
|
462 file_logo="t_logo.png"
|
|
|
463 file_bar="t_bar.png"
|
|
|
464
|
|
|
465 c_samples=[[x[0],x[1],sum(int(i) for i in x[2:])] for x in merge]
|
|
|
466
|
|
|
467 A=[0]*3
|
|
|
468 C=[0]*3
|
|
|
469 G=[0]*3
|
|
|
470 T=[0]*3
|
|
|
471 total_reads=0
|
|
|
472
|
|
|
473 for y in c_samples:
|
|
|
474 if "/" in y[0]:
|
|
|
475 length=[]
|
|
|
476 for x in y[0].split("/"):
|
|
|
477 length.append([len(x.split("_")[-1]),x.split("_")[-1],y[2]])
|
|
|
478
|
|
|
479 best=min(length)
|
|
|
480 total_reads+=best[2]
|
|
|
481 for i in range(3):
|
|
|
482 if i<len(best[1]):
|
|
|
483 if best[1][i] == "A":
|
|
|
484 A[i]+=best[2]
|
|
|
485 elif best[1][i] == "C":
|
|
|
486 C[i]+=best[2]
|
|
|
487 elif best[1][i] == "G":
|
|
|
488 G[i]+=best[2]
|
|
|
489 else:
|
|
|
490 T[i]+=best[2]
|
|
|
491 else:
|
|
|
492 total_reads+=y[2]
|
|
|
493 for i in range(3):
|
|
|
494 if i<len(y[0].split("_")[-1]):
|
|
|
495 if y[0].split("_")[-1][i] == "A":
|
|
|
496 A[i]+=(y[2])
|
|
|
497 elif y[0].split("_")[-1][i] == "C":
|
|
|
498 C[i]+=(y[2])
|
|
|
499 elif y[0].split("_")[-1][i] == "G":
|
|
|
500 G[i]+=(y[2])
|
|
|
501 else:
|
|
|
502 T[i]+=y[2]
|
|
|
503
|
|
|
504 A[:] = [round(x*100,1) / total_reads for x in A]
|
|
|
505 C[:] = [round(x*100,1) / total_reads for x in C]
|
|
|
506 G[:] = [round(x*100,1) / total_reads for x in G]
|
|
|
507 T[:] = [round(x*100,1) / total_reads for x in T]
|
|
|
508
|
|
|
509
|
|
|
510
|
|
|
511 data = {'A':A,'C':C,'G':G,'T':T}
|
|
|
512 df = pd.DataFrame(data, index=[1,2,3])
|
|
|
513 h=df.plot.bar(color=tuple(["g", "b","gold","r"]) )
|
|
|
514 h.grid(axis='y',linewidth=0.2)
|
|
|
515 plt.xticks(rotation=0, ha="right")
|
|
|
516 plt.ylabel("Counts (%)",fontsize=18)
|
|
|
517 plt.xlabel("Numbers of additional nucleotides",fontsize=18)
|
|
|
518 plt.title(titlos,fontsize=20)
|
|
|
519 plt.tight_layout()
|
|
|
520 plt.savefig(file_bar, dpi=300)
|
|
|
521
|
|
|
522 crp_logo = lm.Logo(df, font_name = 'DejaVu Sans')
|
|
|
523 crp_logo.style_spines(visible=False)
|
|
|
524 crp_logo.style_spines(spines=['left', 'bottom'], visible=True)
|
|
|
525 crp_logo.style_xticks(rotation=0, fmt='%d', anchor=0)
|
|
|
526
|
|
|
527 # style using Axes methods
|
|
|
528 crp_logo.ax.set_title(titlos,fontsize=18)
|
|
|
529 crp_logo.ax.set_ylabel("Counts (%)", fontsize=16,labelpad=5)
|
|
|
530 crp_logo.ax.set_xlabel("Numbers of additional nucleotides",fontsize=16, labelpad=5)
|
|
|
531 crp_logo.ax.xaxis.set_ticks_position('none')
|
|
|
532 crp_logo.ax.xaxis.set_tick_params(pad=-1)
|
|
|
533 figure = plt.gcf()
|
|
|
534 figure.set_size_inches(6, 4)
|
|
|
535 crp_logo.fig.savefig(file_logo,dpi=300)
|
|
|
536
|
|
|
537 ##########################################################################################################################################################################################################
|
|
|
538
|
|
|
539 def pdf_before_DE(analysis,group_name1,group_name2):
|
|
|
540
|
|
|
541 # Image extensions
|
|
|
542 if analysis=="2":
|
|
|
543 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_non.png","spider_red.png","spider_non_red.png","c_logo.png","t_logo.png","c_bar.png","t_bar.png")
|
|
|
544 else:
|
|
|
545 image_extensions = ("c_hist_red.png","t_hist_red.png","pie_tem.png","spider_red.png","spider_non_red.png")
|
|
|
546 # This list will hold the images file names
|
|
|
547 images = []
|
|
|
548
|
|
|
549 # Build the image list by merging the glob results (a list of files)
|
|
|
550 # for each extension. We are taking images from current folder.
|
|
|
551 for extension in image_extensions:
|
|
|
552 images.extend(glob.glob(extension))
|
|
|
553
|
|
|
554 # Create instance of FPDF class
|
|
|
555 pdf = FPDF('P', 'in', 'A4')
|
|
|
556 # Add new page. Without this you cannot create the document.
|
|
|
557 pdf.add_page()
|
|
|
558 # Set font to Arial, 'B'old, 16 pts
|
|
|
559 pdf.set_font('Arial', 'B', 20.0)
|
|
|
560
|
|
|
561 # Page header
|
|
16
|
562 pdf.cell(pdf.w-0.5, 0.5, 'IsomiR profile report',align='C')
|
|
3
|
563 pdf.ln(0.7)
|
|
|
564 pdf.set_font('Arial','B', 16.0)
|
|
|
565 pdf.cell(pdf.w-0.5, 0.5, 'sRNA length distribution',align='C')
|
|
|
566
|
|
|
567 # Smaller font for image captions
|
|
|
568 pdf.set_font('Arial', '', 11.0)
|
|
|
569 pdf.ln(0.5)
|
|
|
570
|
|
|
571 yh=FPDF.get_y(pdf)
|
|
|
572 pdf.image(images[0],x=0.3,w=4, h=3)
|
|
|
573 pdf.image(images[1],x=4,y=yh, w=4, h=3)
|
|
|
574 pdf.ln(0.3)
|
|
|
575
|
|
|
576 pdf.cell(0.2)
|
|
16
|
577 pdf.cell(3.0, 0.0, " Mapped and unmapped reads to custom precursor arm reference DB (5p and 3p arms) in "+group_name1.lower())
|
|
3
|
578 pdf.ln(0.2)
|
|
|
579 pdf.cell(0.2)
|
|
16
|
580 pdf.cell(3.0, 0.0, " (left) and "+group_name2.lower()+" (right) groups")
|
|
3
|
581
|
|
|
582 pdf.ln(0.5)
|
|
|
583 h1=FPDF.get_y(pdf)
|
|
|
584 pdf.image(images[2],x=1, w=6.5, h=5)
|
|
|
585 h2=FPDF.get_y(pdf)
|
|
|
586 FPDF.set_y(pdf,h1+0.2)
|
|
|
587 pdf.set_font('Arial','B', 16.0)
|
|
25
|
588 if analysis=="2":
|
|
|
589 pdf.cell(pdf.w-0.5, 0.5, 'Templated and non-templated isomiRs',align='C')
|
|
|
590 else:
|
|
|
591 pdf.cell(pdf.w-0.5, 0.5, 'Templated isomiRs',align='C')
|
|
3
|
592 pdf.set_font('Arial', '', 11.0)
|
|
|
593 FPDF.set_y(pdf,h2)
|
|
|
594 FPDF.set_y(pdf,9.5)
|
|
|
595 pdf.cell(0.2)
|
|
|
596
|
|
|
597 if analysis=="2":
|
|
|
598 pdf.cell(3.0, 0.0, " RefSeq miRNAs, templated isomiRs, non-templated isomiRs and unassigned sequences as percentage")
|
|
|
599 pdf.ln(0.2)
|
|
|
600 pdf.cell(0.2)
|
|
16
|
601 pdf.cell(3.0, 0.0, " of total sRNA reads in "+group_name1.lower()+" (left) and "+group_name2.lower()+" (right) groups")
|
|
3
|
602 else:
|
|
25
|
603 pdf.cell(3.0, 0.0, " RefSeq miRNAS, templated isomiRs and unassigned sequences as percentage of total sRNA reads in")
|
|
3
|
604 pdf.ln(0.2)
|
|
|
605 pdf.cell(0.2)
|
|
16
|
606 pdf.cell(3.0, 0.0, " "+group_name1.lower()+" (left) and "+group_name2.lower() + " (right) groups")
|
|
3
|
607
|
|
|
608 pdf.add_page()
|
|
|
609 pdf.set_font('Arial', 'B', 18.0)
|
|
|
610 pdf.cell(pdf.w-0.5, 0.5, "Templated isomiR subtypes",align='C')
|
|
|
611 pdf.ln(0.7)
|
|
|
612 pdf.set_font('Arial', 'B', 14.0)
|
|
|
613 pdf.cell(pdf.w-0.5, 0.5, "Templated isomiR profile (redundant reads)",align='C')
|
|
|
614 pdf.ln(0.5)
|
|
|
615 pdf.image(images[3],x=1.5, w=5.5, h=4)
|
|
|
616 pdf.ln(0.6)
|
|
|
617 pdf.cell(pdf.w-0.5, 0.0, "Templated isomiR profile (non-redundant reads)",align='C')
|
|
|
618 pdf.set_font('Arial', '', 12.0)
|
|
|
619 pdf.ln(0.2)
|
|
|
620 pdf.image(images[4],x=1.5, w=5.5, h=4)
|
|
|
621 pdf.ln(0.3)
|
|
|
622 pdf.set_font('Arial', '', 11.0)
|
|
|
623 pdf.cell(0.2)
|
|
|
624 pdf.cell(3.0, 0.0, " * IsomiRs potentially generated from multiple loci")
|
|
|
625
|
|
|
626
|
|
|
627 if analysis=="2":
|
|
|
628 pdf.add_page('L')
|
|
|
629
|
|
|
630 pdf.set_font('Arial', 'B', 18.0)
|
|
|
631 pdf.cell(pdf.w-0.5, 0.5, "Non-templated isomiRs",align='C')
|
|
|
632 pdf.ln(0.5)
|
|
|
633 pdf.set_font('Arial', 'B', 14.0)
|
|
|
634 pdf.cell(pdf.w-0.5, 0.5, "3'-end additions to RefSeq miRNAs and templated isomiRs",align='C')
|
|
|
635 pdf.ln(0.7)
|
|
|
636
|
|
|
637 yh=FPDF.get_y(pdf)
|
|
|
638 pdf.image(images[5],x=1.5,w=3.65, h=2.65)
|
|
|
639 pdf.image(images[7],x=6.5,y=yh, w=3.65, h=2.65)
|
|
|
640 pdf.ln(0.5)
|
|
|
641 yh=FPDF.get_y(pdf)
|
|
|
642 pdf.image(images[6],x=1.5,w=3.65, h=2.65)
|
|
|
643 pdf.image(images[8],x=6.5,y=yh, w=3.65, h=2.65)
|
|
|
644
|
|
|
645 pdf.close()
|
|
|
646 pdf.output('report1.pdf','F')
|
|
|
647
|
|
|
648 #############################################################################################################################################################3
|
|
|
649
|
|
|
650
|
