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4
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1 from __future__ import division
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2 import csv
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3 from enum import Enum
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4 import re
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5 import sys
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6 import numpy as np
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7 import pandas as pd
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8 import itertools as it
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9 import scipy.stats as st
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10 import lxml.etree as ET
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11 import math
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12 import utils.general_utils as utils
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13 from PIL import Image
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14 import os
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15 import copy
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16 import argparse
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17 import pyvips
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293
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18 from PIL import Image
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4
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19 from typing import Tuple, Union, Optional, List, Dict
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20 import matplotlib.pyplot as plt
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21
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22 ERRORS = []
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23 ########################## argparse ##########################################
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24 ARGS :argparse.Namespace
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147
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25 def process_args(args:List[str] = None) -> argparse.Namespace:
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4
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26 """
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27 Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code.
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28
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29 Args:
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30 args : Always obtained (in file) from sys.argv
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31
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32 Returns:
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33 Namespace : An object containing the parsed arguments
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34 """
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35 parser = argparse.ArgumentParser(
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36 usage = "%(prog)s [options]",
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37 description = "process some value's genes to create a comparison's map.")
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38
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39 #General:
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40 parser.add_argument(
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41 '-td', '--tool_dir',
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42 type = str,
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43 required = True,
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44 help = 'your tool directory')
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45
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46 parser.add_argument('-on', '--control', type = str)
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47 parser.add_argument('-ol', '--out_log', help = "Output log")
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48
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49 #Computation details:
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50 parser.add_argument(
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51 '-co', '--comparison',
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52 type = str,
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293
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53 default = 'manyvsmany',
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54 choices = ['manyvsmany', 'onevsrest', 'onevsmany'])
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293
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55
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56 parser.add_argument(
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57 '-te' ,'--test',
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58 type = str,
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59 default = 'ks',
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60 choices = ['ks', 'ttest_p', 'ttest_ind', 'wilcoxon', 'mw'],
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61 help = 'Statistical test to use (default: %(default)s)')
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62
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63 parser.add_argument(
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64 '-pv' ,'--pValue',
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65 type = float,
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66 default = 0.1,
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67 help = 'P-Value threshold (default: %(default)s)')
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295
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68
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69 parser.add_argument(
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70 '-adj' ,'--adjusted',
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71 type = utils.Bool("adjusted"), default = False,
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72 help = 'Apply the FDR (Benjamini-Hochberg) correction (default: %(default)s)')
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73
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74 parser.add_argument(
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75 '-fc', '--fChange',
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76 type = float,
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77 default = 1.5,
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78 help = 'Fold-Change threshold (default: %(default)s)')
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79
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80 parser.add_argument(
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81 '-op', '--option',
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82 type = str,
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83 choices = ['datasets', 'dataset_class'],
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84 help='dataset or dataset and class')
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85
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86 parser.add_argument(
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87 '-idf', '--input_data_fluxes',
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88 type = str,
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89 help = 'input dataset fluxes')
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90
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91 parser.add_argument(
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92 '-icf', '--input_class_fluxes',
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93 type = str,
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94 help = 'sample group specification fluxes')
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95
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96 parser.add_argument(
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97 '-idsf', '--input_datas_fluxes',
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98 type = str,
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99 nargs = '+',
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100 help = 'input datasets fluxes')
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101
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102 parser.add_argument(
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103 '-naf', '--names_fluxes',
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104 type = str,
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105 nargs = '+',
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106 help = 'input names fluxes')
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107
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108 #Output:
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109 parser.add_argument(
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110 "-gs", "--generate_svg",
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111 type = utils.Bool("generate_svg"), default = True,
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112 help = "choose whether to generate svg")
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113
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114 parser.add_argument(
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115 "-gp", "--generate_pdf",
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116 type = utils.Bool("generate_pdf"), default = True,
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117 help = "choose whether to generate pdf")
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118
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119 parser.add_argument(
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120 '-cm', '--custom_map',
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121 type = str,
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122 help='custom map to use')
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123
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124 parser.add_argument(
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125 '-mc', '--choice_map',
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126 type = utils.Model, default = utils.Model.HMRcore,
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127 choices = [utils.Model.HMRcore, utils.Model.ENGRO2, utils.Model.Custom])
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128
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129 parser.add_argument(
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130 '-colorm', '--color_map',
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131 type = str,
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132 choices = ["jet", "viridis"])
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147
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133
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134 parser.add_argument(
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135 '-idop', '--output_path',
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136 type = str,
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137 default='result',
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138 help = 'output path for maps')
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139
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147
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140 args :argparse.Namespace = parser.parse_args(args)
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185
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141 args.net = True # TODO SICCOME I FLUSSI POSSONO ESSERE ANCHE NEGATIVI SONO SEMPRE CONSIDERATI NETTI
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142
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143 return args
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293
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144
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4
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145 ############################ dataset input ####################################
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146 def read_dataset(data :str, name :str) -> pd.DataFrame:
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147 """
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148 Tries to read the dataset from its path (data) as a tsv and turns it into a DataFrame.
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149
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150 Args:
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151 data : filepath of a dataset (from frontend input params or literals upon calling)
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152 name : name associated with the dataset (from frontend input params or literals upon calling)
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153
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154 Returns:
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155 pd.DataFrame : dataset in a runtime operable shape
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156
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157 Raises:
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158 sys.exit : if there's no data (pd.errors.EmptyDataError) or if the dataset has less than 2 columns
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159 """
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160 try:
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161 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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162 except pd.errors.EmptyDataError:
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163 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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164 if len(dataset.columns) < 2:
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165 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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166 return dataset
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167
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168 ############################ dataset name #####################################
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169 def name_dataset(name_data :str, count :int) -> str:
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170 """
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171 Produces a unique name for a dataset based on what was provided by the user. The default name for any dataset is "Dataset", thus if the user didn't change it this function appends f"_{count}" to make it unique.
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172
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173 Args:
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174 name_data : name associated with the dataset (from frontend input params)
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175 count : counter from 1 to make these names unique (external)
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176
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177 Returns:
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178 str : the name made unique
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179 """
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180 if str(name_data) == 'Dataset':
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181 return str(name_data) + '_' + str(count)
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182 else:
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183 return str(name_data)
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184
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185 ############################ map_methods ######################################
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186 FoldChange = Union[float, int, str] # Union[float, Literal[0, "-INF", "INF"]]
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187 def fold_change(avg1 :float, avg2 :float) -> FoldChange:
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188 """
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189 Calculates the fold change between two gene expression values.
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190
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191 Args:
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192 avg1 : average expression value from one dataset avg2 : average expression value from the other dataset
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193
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194 Returns:
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195 FoldChange :
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196 0 : when both input values are 0
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197 "-INF" : when avg1 is 0
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198 "INF" : when avg2 is 0
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199 float : for any other combination of values
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200 """
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201 if avg1 == 0 and avg2 == 0:
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202 return 0
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203 elif avg1 == 0:
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204 return '-INF'
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205 elif avg2 == 0:
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206 return 'INF'
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207 else: # (threshold_F_C - 1) / (abs(threshold_F_C) + 1) con threshold_F_C > 1
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208 return (avg1 - avg2) / (abs(avg1) + abs(avg2))
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209
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210 def getElementById(reactionId :str, metabMap :ET.ElementTree) -> utils.Result[ET.Element, utils.Result.ResultErr]:
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211 """
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212 Finds any element in the given map with the given ID. ID uniqueness in an svg file is recommended but
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213 not enforced, if more than one element with the exact ID is found only the first will be returned.
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214
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215 Args:
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216 reactionId (str): exact ID of the requested element.
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217 metabMap (ET.ElementTree): metabolic map containing the element.
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218
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219 Returns:
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220 utils.Result[ET.Element, ResultErr]: result of the search, either the first match found or a ResultErr.
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221 """
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222 return utils.Result.Ok(
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223 f"//*[@id=\"{reactionId}\"]").map(
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224 lambda xPath : metabMap.xpath(xPath)[0]).mapErr(
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225 lambda _ : utils.Result.ResultErr(f"No elements with ID \"{reactionId}\" found in map"))
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226 # ^^^ we shamelessly ignore the contents of the IndexError, it offers nothing to the user.
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227
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228 def styleMapElement(element :ET.Element, styleStr :str) -> None:
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229 currentStyles :str = element.get("style", "")
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230 if re.search(r";stroke:[^;]+;stroke-width:[^;]+;stroke-dasharray:[^;]+$", currentStyles):
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231 currentStyles = ';'.join(currentStyles.split(';')[:-3])
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232
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233 element.set("style", currentStyles + styleStr)
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234
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235 class ReactionDirection(Enum):
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236 Unknown = ""
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237 Direct = "_F"
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238 Inverse = "_B"
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239
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240 @classmethod
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241 def fromDir(cls, s :str) -> "ReactionDirection":
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242 # vvv as long as there's so few variants I actually condone the if spam:
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243 if s == ReactionDirection.Direct.value: return ReactionDirection.Direct
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244 if s == ReactionDirection.Inverse.value: return ReactionDirection.Inverse
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245 return ReactionDirection.Unknown
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246
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247 @classmethod
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248 def fromReactionId(cls, reactionId :str) -> "ReactionDirection":
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249 return ReactionDirection.fromDir(reactionId[-2:])
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250
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251 def getArrowBodyElementId(reactionId :str) -> str:
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252 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
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253 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: reactionId = reactionId[:-2]
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254 return f"R_{reactionId}"
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255
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256 def getArrowHeadElementId(reactionId :str) -> Tuple[str, str]:
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257 """
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258 We attempt extracting the direction information from the provided reaction ID, if unsuccessful we provide the IDs of both directions.
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259
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260 Args:
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261 reactionId : the provided reaction ID.
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262
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263 Returns:
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264 Tuple[str, str]: either a single str ID for the correct arrow head followed by an empty string or both options to try.
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265 """
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266 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
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267 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: return reactionId[:-3:-1] + reactionId[:-2], ""
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268 return f"F_{reactionId}", f"B_{reactionId}"
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269
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270 class ArrowColor(Enum):
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271 """
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272 Encodes possible arrow colors based on their meaning in the enrichment process.
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273 """
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274 Invalid = "#BEBEBE" # gray, fold-change under treshold
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275 Transparent = "#ffffff00" # white, not significant p-value
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276 UpRegulated = "#ecac68" # red, up-regulated reaction
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277 DownRegulated = "#6495ed" # blue, down-regulated reaction
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278
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279 UpRegulatedInv = "#FF0000"
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280 # ^^^ different shade of red (actually orange), up-regulated net value for a reversible reaction with
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281 # conflicting enrichment in the two directions.
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282
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283 DownRegulatedInv = "#0000FF"
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284 # ^^^ different shade of blue (actually purple), down-regulated net value for a reversible reaction with
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285 # conflicting enrichment in the two directions.
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286
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287 @classmethod
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288 def fromFoldChangeSign(cls, foldChange :float, *, useAltColor = False) -> "ArrowColor":
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289 colors = (cls.DownRegulated, cls.DownRegulatedInv) if foldChange < 0 else (cls.UpRegulated, cls.UpRegulatedInv)
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290 return colors[useAltColor]
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291
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292 def __str__(self) -> str: return self.value
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293
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294 class Arrow:
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295 """
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296 Models the properties of a reaction arrow that change based on enrichment.
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297 """
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298 MIN_W = 2
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299 MAX_W = 12
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300
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301 def __init__(self, width :int, col: ArrowColor, *, isDashed = False) -> None:
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302 """
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303 (Private) Initializes an instance of Arrow.
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304
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305 Args:
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306 width : width of the arrow, ideally to be kept within Arrow.MIN_W and Arrow.MAX_W (not enforced).
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307 col : color of the arrow.
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308 isDashed : whether the arrow should be dashed, meaning the associated pValue resulted not significant.
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309
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310 Returns:
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311 None : practically, a Arrow instance.
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312 """
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313 self.w = width
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314 self.col = col
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315 self.dash = isDashed
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316
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317 def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
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318 if getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).isErr:
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319 ERRORS.append(reactionId)
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320
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321 def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
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322 if not mindReactionDir:
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323 return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
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324
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325 # Now we style the arrow head(s):
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326 idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
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327 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
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328 if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
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329
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330 def styleReactionElementsMeanMedian(self, metabMap :ET.ElementTree, reactionId :str, isNegative:bool) -> None:
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331
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332 self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
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333 idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
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334
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335 if(isNegative):
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336 self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
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337 self.col = ArrowColor.Transparent
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338 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True)) #trasp
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339 else:
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340 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
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341 self.col = ArrowColor.Transparent
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342 self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True)) #trasp
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343
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344
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345
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346 def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
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347 """
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348 Computes the reaction ID as encoded in the map for a given reaction ID from the dataset.
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349
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350 Args:
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351 reactionId: the reaction ID, as encoded in the dataset.
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352 mindReactionDir: if True forward (F_) and backward (B_) directions will be encoded in the result.
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353
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354 Returns:
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355 str : the ID of an arrow's body or tips in the map.
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356 """
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357 # we assume the reactionIds also don't encode reaction dir if they don't mind it when styling the map.
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358 if not mindReactionDir: return "R_" + reactionId
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359
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360 #TODO: this is clearly something we need to make consistent in fluxes
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361 return (reactionId[:-3:-1] + reactionId[:-2]) if reactionId[:-2] in ["_F", "_B"] else f"F_{reactionId}" # "Pyr_F" --> "F_Pyr"
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362
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363 def toStyleStr(self, *, downSizedForTips = False) -> str:
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364 """
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365 Collapses the styles of this Arrow into a str, ready to be applied as part of the "style" property on an svg element.
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366
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367 Returns:
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368 str : the styles string.
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369 """
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370 width = self.w
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371 if downSizedForTips: width *= 0.8
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372 return f";stroke:{self.col};stroke-width:{width};stroke-dasharray:{'5,5' if self.dash else 'none'}"
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373
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374 # vvv These constants could be inside the class itself a static properties, but python
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375 # was built by brainless organisms so here we are!
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376 INVALID_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid)
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377 INSIGNIFICANT_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid, isDashed = True)
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378
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379 def applyFluxesEnrichmentToMap(fluxesEnrichmentRes :Dict[str, Union[Tuple[float, FoldChange], Tuple[float, FoldChange, float, float]]], metabMap :ET.ElementTree, maxNumericZScore :float) -> None:
|
|
|
380 """
|
|
|
381 Applies fluxes enrichment results to the provided metabolic map.
|
|
|
382
|
|
|
383 Args:
|
|
|
384 fluxesEnrichmentRes : fluxes enrichment results.
|
|
|
385 metabMap : the metabolic map to edit.
|
|
|
386 maxNumericZScore : biggest finite z-score value found.
|
|
|
387
|
|
|
388 Side effects:
|
|
|
389 metabMap : mut
|
|
|
390
|
|
|
391 Returns:
|
|
|
392 None
|
|
|
393 """
|
|
|
394 for reactionId, values in fluxesEnrichmentRes.items():
|
|
|
395 pValue = values[0]
|
|
|
396 foldChange = values[1]
|
|
|
397 z_score = values[2]
|
|
|
398
|
|
275
|
399 if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)):
|
|
|
400 continue
|
|
|
401
|
|
4
|
402 if isinstance(foldChange, str): foldChange = float(foldChange)
|
|
|
403 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
|
|
|
404 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
|
|
|
405 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
|
|
|
406
|
|
|
407 continue
|
|
|
408
|
|
|
409 if abs(foldChange) < (ARGS.fChange - 1) / (abs(ARGS.fChange) + 1):
|
|
|
410 INVALID_ARROW.styleReactionElements(metabMap, reactionId)
|
|
|
411 INVALID_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
|
|
|
412
|
|
|
413 continue
|
|
|
414
|
|
|
415 width = Arrow.MAX_W
|
|
293
|
416 if not math.isinf(z_score):
|
|
4
|
417 try:
|
|
293
|
418 width = min(
|
|
|
419 max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W),
|
|
|
420 Arrow.MAX_W)
|
|
4
|
421
|
|
|
422 except ZeroDivisionError: pass
|
|
185
|
423 # TODO CHECK RV
|
|
4
|
424 #if not reactionId.endswith("_RV"): # RV stands for reversible reactions
|
|
197
|
425 # Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId)
|
|
|
426 # continue
|
|
4
|
427
|
|
|
428 #reactionId = reactionId[:-3] # Remove "_RV"
|
|
|
429
|
|
|
430 inversionScore = (values[3] < 0) + (values[4] < 0) # Compacts the signs of averages into 1 easy to check score
|
|
|
431 if inversionScore == 2: foldChange *= -1
|
|
|
432 # ^^^ Style the inverse direction with the opposite sign netValue
|
|
|
433
|
|
|
434 # If the score is 1 (opposite signs) we use alternative colors vvv
|
|
|
435 arrow = Arrow(width, ArrowColor.fromFoldChangeSign(foldChange, useAltColor = inversionScore == 1))
|
|
|
436
|
|
|
437 # vvv These 2 if statements can both be true and can both happen
|
|
|
438 if ARGS.net: # style arrow head(s):
|
|
|
439 arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
|
|
|
440 arrow.applyTo(("F_" if inversionScore == 2 else "B_") + reactionId, metabMap, f";stroke:{ArrowColor.Transparent};stroke-width:0;stroke-dasharray:None")
|
|
|
441
|
|
186
|
442 arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
|
|
4
|
443
|
|
|
444
|
|
|
445 ############################ split class ######################################
|
|
|
446 def split_class(classes :pd.DataFrame, resolve_rules :Dict[str, List[float]]) -> Dict[str, List[List[float]]]:
|
|
|
447 """
|
|
|
448 Generates a :dict that groups together data from a :DataFrame based on classes the data is related to.
|
|
|
449
|
|
|
450 Args:
|
|
|
451 classes : a :DataFrame of only string values, containing class information (rows) and keys to query the resolve_rules :dict
|
|
|
452 resolve_rules : a :dict containing :float data
|
|
|
453
|
|
|
454 Returns:
|
|
|
455 dict : the dict with data grouped by class
|
|
|
456
|
|
|
457 Side effects:
|
|
|
458 classes : mut
|
|
|
459 """
|
|
|
460 class_pat :Dict[str, List[List[float]]] = {}
|
|
|
461 for i in range(len(classes)):
|
|
|
462 classe :str = classes.iloc[i, 1]
|
|
|
463 if pd.isnull(classe): continue
|
|
|
464
|
|
|
465 l :List[List[float]] = []
|
|
|
466 for j in range(i, len(classes)):
|
|
|
467 if classes.iloc[j, 1] == classe:
|
|
|
468 pat_id :str = classes.iloc[j, 0]
|
|
|
469 tmp = resolve_rules.get(pat_id, None)
|
|
|
470 if tmp != None:
|
|
|
471 l.append(tmp)
|
|
|
472 classes.iloc[j, 1] = None
|
|
|
473
|
|
|
474 if l:
|
|
|
475 class_pat[classe] = list(map(list, zip(*l)))
|
|
|
476 continue
|
|
|
477
|
|
|
478 utils.logWarning(
|
|
|
479 f"Warning: no sample found in class \"{classe}\", the class has been disregarded", ARGS.out_log)
|
|
|
480
|
|
|
481 return class_pat
|
|
|
482
|
|
|
483 ############################ conversion ##############################################
|
|
|
484 #conversion from svg to png
|
|
|
485 def svg_to_png_with_background(svg_path :utils.FilePath, png_path :utils.FilePath, dpi :int = 72, scale :int = 1, size :Optional[float] = None) -> None:
|
|
|
486 """
|
|
|
487 Internal utility to convert an SVG to PNG (forced opaque) to aid in PDF conversion.
|
|
|
488
|
|
|
489 Args:
|
|
|
490 svg_path : path to SVG file
|
|
|
491 png_path : path for new PNG file
|
|
|
492 dpi : dots per inch of the generated PNG
|
|
|
493 scale : scaling factor for the generated PNG, computed internally when a size is provided
|
|
|
494 size : final effective width of the generated PNG
|
|
|
495
|
|
|
496 Returns:
|
|
|
497 None
|
|
|
498 """
|
|
|
499 if size:
|
|
|
500 image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=1)
|
|
|
501 scale = size / image.width
|
|
|
502 image = image.resize(scale)
|
|
|
503 else:
|
|
|
504 image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=scale)
|
|
|
505
|
|
|
506 white_background = pyvips.Image.black(image.width, image.height).new_from_image([255, 255, 255])
|
|
|
507 white_background = white_background.affine([scale, 0, 0, scale])
|
|
|
508
|
|
|
509 if white_background.bands != image.bands:
|
|
|
510 white_background = white_background.extract_band(0)
|
|
|
511
|
|
|
512 composite_image = white_background.composite2(image, 'over')
|
|
|
513 composite_image.write_to_file(png_path.show())
|
|
|
514
|
|
|
515 #funzione unica, lascio fuori i file e li passo in input
|
|
|
516 #conversion from png to pdf
|
|
|
517 def convert_png_to_pdf(png_file :utils.FilePath, pdf_file :utils.FilePath) -> None:
|
|
|
518 """
|
|
|
519 Internal utility to convert a PNG to PDF to aid from SVG conversion.
|
|
|
520
|
|
|
521 Args:
|
|
|
522 png_file : path to PNG file
|
|
|
523 pdf_file : path to new PDF file
|
|
|
524
|
|
|
525 Returns:
|
|
|
526 None
|
|
|
527 """
|
|
|
528 image = Image.open(png_file.show())
|
|
|
529 image = image.convert("RGB")
|
|
|
530 image.save(pdf_file.show(), "PDF", resolution=100.0)
|
|
|
531
|
|
|
532 #function called to reduce redundancy in the code
|
|
|
533 def convert_to_pdf(file_svg :utils.FilePath, file_png :utils.FilePath, file_pdf :utils.FilePath) -> None:
|
|
|
534 """
|
|
|
535 Converts the SVG map at the provided path to PDF.
|
|
|
536
|
|
|
537 Args:
|
|
|
538 file_svg : path to SVG file
|
|
|
539 file_png : path to PNG file
|
|
|
540 file_pdf : path to new PDF file
|
|
|
541
|
|
|
542 Returns:
|
|
|
543 None
|
|
|
544 """
|
|
|
545 svg_to_png_with_background(file_svg, file_png)
|
|
|
546 try:
|
|
|
547 convert_png_to_pdf(file_png, file_pdf)
|
|
|
548 print(f'PDF file {file_pdf.filePath} successfully generated.')
|
|
|
549
|
|
|
550 except Exception as e:
|
|
|
551 raise utils.DataErr(file_pdf.show(), f'Error generating PDF file: {e}')
|
|
|
552
|
|
|
553 ############################ map ##############################################
|
|
|
554 def buildOutputPath(dataset1Name :str, dataset2Name = "rest", *, details = "", ext :utils.FileFormat) -> utils.FilePath:
|
|
|
555 """
|
|
|
556 Builds a FilePath instance from the names of confronted datasets ready to point to a location in the
|
|
|
557 "result/" folder, used by this tool for output files in collections.
|
|
|
558
|
|
|
559 Args:
|
|
|
560 dataset1Name : _description_
|
|
|
561 dataset2Name : _description_. Defaults to "rest".
|
|
|
562 details : _description_
|
|
|
563 ext : _description_
|
|
|
564
|
|
|
565 Returns:
|
|
|
566 utils.FilePath : _description_
|
|
|
567 """
|
|
|
568 # This function returns a util data structure but is extremely specific to this module.
|
|
|
569 # RAS also uses collections as output and as such might benefit from a method like this, but I'd wait
|
|
|
570 # TODO: until a third tool with multiple outputs appears before porting this to utils.
|
|
|
571 return utils.FilePath(
|
|
|
572 f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
|
|
|
573 # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
|
|
|
574 # all output files: I don't care, this was never the performance bottleneck of the tool and
|
|
|
575 # there is no other net gain in saving and re-using the built string.
|
|
|
576 ext,
|
|
147
|
577 prefix = ARGS.output_path)
|
|
4
|
578
|
|
|
579 FIELD_NOT_AVAILABLE = '/'
|
|
|
580 def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
|
|
|
581 fieldsAmt = len(fieldNames)
|
|
|
582 with open(outPath.show(), "w", newline = "") as fd:
|
|
|
583 writer = csv.DictWriter(fd, fieldnames = fieldNames, delimiter = '\t')
|
|
|
584 writer.writeheader()
|
|
|
585
|
|
|
586 for row in rows:
|
|
|
587 sizeMismatch = fieldsAmt - len(row)
|
|
|
588 if sizeMismatch > 0: row.extend([FIELD_NOT_AVAILABLE] * sizeMismatch)
|
|
|
589 writer.writerow({ field : data for field, data in zip(fieldNames, row) })
|
|
|
590
|
|
|
591 OldEnrichedScores = Dict[str, List[Union[float, FoldChange]]] #TODO: try to use Tuple whenever possible
|
|
|
592 def writeTabularResult(enrichedScores : OldEnrichedScores, outPath :utils.FilePath) -> None:
|
|
199
|
593 fieldNames = ["ids", "P_Value", "fold change", "z-score"]
|
|
4
|
594 fieldNames.extend(["average_1", "average_2"])
|
|
|
595
|
|
|
596 writeToCsv([ [reactId] + values for reactId, values in enrichedScores.items() ], fieldNames, outPath)
|
|
|
597
|
|
|
598 def temp_thingsInCommon(tmp :Dict[str, List[Union[float, FoldChange]]], core_map :ET.ElementTree, max_z_score :float, dataset1Name :str, dataset2Name = "rest") -> None:
|
|
|
599 # this function compiles the things always in common between comparison modes after enrichment.
|
|
|
600 # TODO: organize, name better.
|
|
|
601 writeTabularResult(tmp, buildOutputPath(dataset1Name, dataset2Name, details = "Tabular Result", ext = utils.FileFormat.TSV))
|
|
|
602 for reactId, enrichData in tmp.items(): tmp[reactId] = tuple(enrichData)
|
|
|
603 applyFluxesEnrichmentToMap(tmp, core_map, max_z_score)
|
|
|
604
|
|
|
605 def computePValue(dataset1Data: List[float], dataset2Data: List[float]) -> Tuple[float, float]:
|
|
|
606 """
|
|
|
607 Computes the statistical significance score (P-value) of the comparison between coherent data
|
|
|
608 from two datasets. The data is supposed to, in both datasets:
|
|
|
609 - be related to the same reaction ID;
|
|
|
610 - be ordered by sample, such that the item at position i in both lists is related to the
|
|
|
611 same sample or cell line.
|
|
|
612
|
|
|
613 Args:
|
|
|
614 dataset1Data : data from the 1st dataset.
|
|
|
615 dataset2Data : data from the 2nd dataset.
|
|
|
616
|
|
|
617 Returns:
|
|
|
618 tuple: (P-value, Z-score)
|
|
293
|
619 - P-value from the selected test on the provided data.
|
|
4
|
620 - Z-score of the difference between means of the two datasets.
|
|
|
621 """
|
|
293
|
622
|
|
|
623 match ARGS.test:
|
|
|
624 case "ks":
|
|
|
625 # Perform Kolmogorov-Smirnov test
|
|
|
626 _, p_value = st.ks_2samp(dataset1Data, dataset2Data)
|
|
|
627 case "ttest_p":
|
|
|
628 # Perform t-test for paired samples
|
|
|
629 _, p_value = st.ttest_rel(dataset1Data, dataset2Data)
|
|
|
630 case "ttest_ind":
|
|
|
631 # Perform t-test for independent samples
|
|
|
632 _, p_value = st.ttest_ind(dataset1Data, dataset2Data)
|
|
|
633 case "wilcoxon":
|
|
|
634 # Perform Wilcoxon signed-rank test
|
|
|
635 _, p_value = st.wilcoxon(dataset1Data, dataset2Data)
|
|
|
636 case "mw":
|
|
|
637 # Perform Mann-Whitney U test
|
|
|
638 _, p_value = st.mannwhitneyu(dataset1Data, dataset2Data)
|
|
4
|
639
|
|
|
640 # Calculate means and standard deviations
|
|
242
|
641 mean1 = np.nanmean(dataset1Data)
|
|
|
642 mean2 = np.nanmean(dataset2Data)
|
|
244
|
643 std1 = np.nanstd(dataset1Data, ddof=1)
|
|
|
644 std2 = np.nanstd(dataset2Data, ddof=1)
|
|
4
|
645
|
|
|
646 n1 = len(dataset1Data)
|
|
|
647 n2 = len(dataset2Data)
|
|
|
648
|
|
|
649 # Calculate Z-score
|
|
|
650 z_score = (mean1 - mean2) / np.sqrt((std1**2 / n1) + (std2**2 / n2))
|
|
|
651
|
|
|
652 return p_value, z_score
|
|
|
653
|
|
|
654 def compareDatasetPair(dataset1Data :List[List[float]], dataset2Data :List[List[float]], ids :List[str]) -> Tuple[Dict[str, List[Union[float, FoldChange]]], float]:
|
|
|
655 #TODO: the following code still suffers from "dumbvarnames-osis"
|
|
295
|
656 comparisonResult :Dict[str, List[Union[float, FoldChange]]] = {}
|
|
4
|
657 count = 0
|
|
|
658 max_z_score = 0
|
|
|
659 for l1, l2 in zip(dataset1Data, dataset2Data):
|
|
|
660 reactId = ids[count]
|
|
|
661 count += 1
|
|
|
662 if not reactId: continue # we skip ids that have already been processed
|
|
|
663
|
|
|
664 try:
|
|
|
665 p_value, z_score = computePValue(l1, l2)
|
|
|
666 avg1 = sum(l1) / len(l1)
|
|
|
667 avg2 = sum(l2) / len(l2)
|
|
197
|
668 f_c = fold_change(avg1, avg2)
|
|
293
|
669 if np.isfinite(z_score) and max_z_score < abs(z_score): max_z_score = abs(z_score)
|
|
211
|
670
|
|
295
|
671 comparisonResult[reactId] = [float(p_value), f_c, z_score, avg1, avg2]
|
|
4
|
672 except (TypeError, ZeroDivisionError): continue
|
|
295
|
673
|
|
|
674 # Apply multiple testing correction if set by the user
|
|
|
675 if ARGS.adjusted:
|
|
|
676
|
|
|
677 # Retrive the p-values from the comparisonResult dictionary
|
|
|
678 reactIds = list(comparisonResult.keys())
|
|
|
679 pValues = [comparisonResult[reactId][0] for reactId in reactIds]
|
|
|
680
|
|
|
681 # Apply the Benjamini-Hochberg correction and update
|
|
|
682 adjustedPValues = st.multipletests(pValues, method="fdr_bh")[1]
|
|
|
683 for i, reactId in enumerate(reactIds):
|
|
|
684 comparisonResult[reactId][0] = adjustedPValues[i]
|
|
4
|
685
|
|
295
|
686 return comparisonResult, max_z_score
|
|
4
|
687
|
|
151
|
688 def computeEnrichment(class_pat :Dict[str, List[List[float]]], ids :List[str]) -> List[Tuple[str, str, dict, float]]:
|
|
4
|
689 """
|
|
|
690 Compares clustered data based on a given comparison mode and applies enrichment-based styling on the
|
|
|
691 provided metabolic map.
|
|
|
692
|
|
|
693 Args:
|
|
|
694 class_pat : the clustered data.
|
|
|
695 ids : ids for data association.
|
|
|
696
|
|
|
697
|
|
|
698 Returns:
|
|
148
|
699 List[Tuple[str, str, dict, float]]: List of tuples with pairs of dataset names, comparison dictionary, and max z-score.
|
|
4
|
700
|
|
|
701 Raises:
|
|
|
702 sys.exit : if there are less than 2 classes for comparison
|
|
151
|
703
|
|
4
|
704 """
|
|
|
705 class_pat = { k.strip() : v for k, v in class_pat.items() }
|
|
|
706 #TODO: simplfy this stuff vvv and stop using sys.exit (raise the correct utils error)
|
|
|
707 if (not class_pat) or (len(class_pat.keys()) < 2): sys.exit('Execution aborted: classes provided for comparisons are less than two\n')
|
|
|
708
|
|
148
|
709 enrichment_results = []
|
|
|
710
|
|
|
711
|
|
4
|
712 if ARGS.comparison == "manyvsmany":
|
|
|
713 for i, j in it.combinations(class_pat.keys(), 2):
|
|
|
714 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids)
|
|
148
|
715 enrichment_results.append((i, j, comparisonDict, max_z_score))
|
|
4
|
716
|
|
|
717 elif ARGS.comparison == "onevsrest":
|
|
|
718 for single_cluster in class_pat.keys():
|
|
148
|
719 rest = [item for k, v in class_pat.items() if k != single_cluster for item in v]
|
|
211
|
720
|
|
4
|
721 comparisonDict, max_z_score = compareDatasetPair(class_pat.get(single_cluster), rest, ids)
|
|
148
|
722 enrichment_results.append((single_cluster, "rest", comparisonDict, max_z_score))
|
|
4
|
723
|
|
|
724 elif ARGS.comparison == "onevsmany":
|
|
|
725 controlItems = class_pat.get(ARGS.control)
|
|
|
726 for otherDataset in class_pat.keys():
|
|
148
|
727 if otherDataset == ARGS.control:
|
|
|
728 continue
|
|
4
|
729 comparisonDict, max_z_score = compareDatasetPair(controlItems, class_pat.get(otherDataset), ids)
|
|
148
|
730 enrichment_results.append((ARGS.control, otherDataset, comparisonDict, max_z_score))
|
|
|
731 return enrichment_results
|
|
4
|
732
|
|
|
733 def createOutputMaps(dataset1Name :str, dataset2Name :str, core_map :ET.ElementTree) -> None:
|
|
148
|
734 svgFilePath = buildOutputPath(dataset1Name, dataset2Name, details="SVG Map", ext=utils.FileFormat.SVG)
|
|
4
|
735 utils.writeSvg(svgFilePath, core_map)
|
|
|
736
|
|
|
737 if ARGS.generate_pdf:
|
|
148
|
738 pngPath = buildOutputPath(dataset1Name, dataset2Name, details="PNG Map", ext=utils.FileFormat.PNG)
|
|
|
739 pdfPath = buildOutputPath(dataset1Name, dataset2Name, details="PDF Map", ext=utils.FileFormat.PDF)
|
|
|
740 convert_to_pdf(svgFilePath, pngPath, pdfPath)
|
|
4
|
741
|
|
148
|
742 if not ARGS.generate_svg:
|
|
|
743 os.remove(svgFilePath.show())
|
|
4
|
744
|
|
|
745 ClassPat = Dict[str, List[List[float]]]
|
|
|
746 def getClassesAndIdsFromDatasets(datasetsPaths :List[str], datasetPath :str, classPath :str, names :List[str]) -> Tuple[List[str], ClassPat]:
|
|
|
747 # TODO: I suggest creating dicts with ids as keys instead of keeping class_pat and ids separate,
|
|
|
748 # for the sake of everyone's sanity.
|
|
|
749 class_pat :ClassPat = {}
|
|
|
750 if ARGS.option == 'datasets':
|
|
|
751 num = 1 #TODO: the dataset naming function could be a generator
|
|
|
752 for path, name in zip(datasetsPaths, names):
|
|
|
753 name = name_dataset(name, num)
|
|
|
754 resolve_rules_float, ids = getDatasetValues(path, name)
|
|
|
755 if resolve_rules_float != None:
|
|
|
756 class_pat[name] = list(map(list, zip(*resolve_rules_float.values())))
|
|
|
757
|
|
|
758 num += 1
|
|
|
759
|
|
|
760 elif ARGS.option == "dataset_class":
|
|
|
761 classes = read_dataset(classPath, "class")
|
|
|
762 classes = classes.astype(str)
|
|
235
|
763 resolve_rules_float, ids = getDatasetValues(datasetPath, "Dataset Class (not actual name)")
|
|
293
|
764 #check if classes have match on ids
|
|
234
|
765 if not all(classes.iloc[:, 0].isin(ids)):
|
|
|
766 utils.logWarning(
|
|
|
767 "No match between classes and sample IDs", ARGS.out_log)
|
|
4
|
768 if resolve_rules_float != None: class_pat = split_class(classes, resolve_rules_float)
|
|
|
769
|
|
|
770 return ids, class_pat
|
|
|
771 #^^^ TODO: this could be a match statement over an enum, make it happen future marea dev with python 3.12! (it's why I kept the ifs)
|
|
|
772
|
|
|
773 #TODO: create these damn args as FilePath objects
|
|
|
774 def getDatasetValues(datasetPath :str, datasetName :str) -> Tuple[ClassPat, List[str]]:
|
|
|
775 """
|
|
|
776 Opens the dataset at the given path and extracts the values (expected nullable numerics) and the IDs.
|
|
|
777
|
|
|
778 Args:
|
|
|
779 datasetPath : path to the dataset
|
|
|
780 datasetName (str): dataset name, used in error reporting
|
|
|
781
|
|
|
782 Returns:
|
|
|
783 Tuple[ClassPat, List[str]]: values and IDs extracted from the dataset
|
|
|
784 """
|
|
|
785 dataset = read_dataset(datasetPath, datasetName)
|
|
240
|
786
|
|
|
787 # Ensure the first column is treated as the reaction name
|
|
|
788 dataset = dataset.set_index(dataset.columns[0])
|
|
|
789
|
|
|
790 # Check if required reactions exist in the dataset
|
|
|
791 required_reactions = ['EX_lac__L_e', 'EX_glc__D_e', 'EX_gln__L_e', 'EX_glu__L_e']
|
|
|
792 missing_reactions = [reaction for reaction in required_reactions if reaction not in dataset.index]
|
|
|
793
|
|
|
794 if missing_reactions:
|
|
|
795 sys.exit(f'Execution aborted: Missing required reactions {missing_reactions} in {datasetName}\n')
|
|
|
796
|
|
|
797 # Calculate new rows using safe division
|
|
|
798 lact_glc = np.divide(
|
|
241
|
799 np.clip(dataset.loc['EX_lac__L_e'].to_numpy(), a_min=0, a_max=None),
|
|
|
800 np.clip(dataset.loc['EX_glc__D_e'].to_numpy(), a_min=None, a_max=0),
|
|
|
801 out=np.full_like(dataset.loc['EX_lac__L_e'].to_numpy(), np.nan), # Prepara un array con NaN come output di default
|
|
|
802 where=dataset.loc['EX_glc__D_e'].to_numpy() != 0 # Condizione per evitare la divisione per zero
|
|
240
|
803 )
|
|
|
804 lact_gln = np.divide(
|
|
241
|
805 np.clip(dataset.loc['EX_lac__L_e'].to_numpy(), a_min=0, a_max=None),
|
|
|
806 np.clip(dataset.loc['EX_gln__L_e'].to_numpy(), a_min=None, a_max=0),
|
|
|
807 out=np.full_like(dataset.loc['EX_lac__L_e'].to_numpy(), np.nan),
|
|
|
808 where=dataset.loc['EX_gln__L_e'].to_numpy() != 0
|
|
|
809 )
|
|
|
810 lact_o2 = np.divide(
|
|
|
811 np.clip(dataset.loc['EX_lac__L_e'].to_numpy(), a_min=0, a_max=None),
|
|
|
812 np.clip(dataset.loc['EX_o2_e'].to_numpy(), a_min=None, a_max=0),
|
|
|
813 out=np.full_like(dataset.loc['EX_lac__L_e'].to_numpy(), np.nan),
|
|
|
814 where=dataset.loc['EX_o2_e'].to_numpy() != 0
|
|
240
|
815 )
|
|
|
816 glu_gln = np.divide(
|
|
241
|
817 dataset.loc['EX_glu__L_e'].to_numpy(),
|
|
|
818 np.clip(dataset.loc['EX_gln__L_e'].to_numpy(), a_min=None, a_max=0),
|
|
|
819 out=np.full_like(dataset.loc['EX_lac__L_e'].to_numpy(), np.nan),
|
|
|
820 where=dataset.loc['EX_gln__L_e'].to_numpy() != 0
|
|
240
|
821 )
|
|
|
822
|
|
253
|
823
|
|
246
|
824 values = {'lact_glc': lact_glc, 'lact_gln': lact_gln, 'lact_o2': lact_o2, 'glu_gln': glu_gln}
|
|
|
825
|
|
|
826 # Sostituzione di inf e NaN con 0 se necessario
|
|
253
|
827 for key in values:
|
|
|
828 values[key] = np.nan_to_num(values[key], nan=0.0, posinf=0.0, neginf=0.0)
|
|
245
|
829
|
|
246
|
830 # Creazione delle nuove righe da aggiungere al dataset
|
|
240
|
831 new_rows = pd.DataFrame({
|
|
246
|
832 dataset.index.name: ['LactGlc', 'LactGln', 'LactO2', 'GluGln'],
|
|
|
833 **{col: [values['lact_glc'][i], values['lact_gln'][i], values['lact_o2'][i], values['glu_gln'][i]]
|
|
|
834 for i, col in enumerate(dataset.columns)}
|
|
240
|
835 })
|
|
|
836
|
|
293
|
837 #print(new_rows)
|
|
254
|
838
|
|
246
|
839 # Ritorna il dataset originale con le nuove righe
|
|
240
|
840 dataset.reset_index(inplace=True)
|
|
|
841 dataset = pd.concat([dataset, new_rows], ignore_index=True)
|
|
|
842
|
|
4
|
843 IDs = pd.Series.tolist(dataset.iloc[:, 0].astype(str))
|
|
|
844
|
|
|
845 dataset = dataset.drop(dataset.columns[0], axis = "columns").to_dict("list")
|
|
|
846 return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs
|
|
|
847
|
|
|
848 def rgb_to_hex(rgb):
|
|
|
849 """
|
|
|
850 Convert RGB values (0-1 range) to hexadecimal color format.
|
|
|
851
|
|
|
852 Args:
|
|
|
853 rgb (numpy.ndarray): An array of RGB color components (in the range [0, 1]).
|
|
|
854
|
|
|
855 Returns:
|
|
|
856 str: The color in hexadecimal format (e.g., '#ff0000' for red).
|
|
|
857 """
|
|
|
858 # Convert RGB values (0-1 range) to hexadecimal format
|
|
|
859 rgb = (np.array(rgb) * 255).astype(int)
|
|
|
860 return '#{:02x}{:02x}{:02x}'.format(rgb[0], rgb[1], rgb[2])
|
|
|
861
|
|
|
862 def save_colormap_image(min_value: float, max_value: float, path: utils.FilePath, colorMap:str="viridis"):
|
|
|
863 """
|
|
|
864 Create and save an image of the colormap showing the gradient and its range.
|
|
|
865
|
|
|
866 Args:
|
|
|
867 min_value (float): The minimum value of the colormap range.
|
|
|
868 max_value (float): The maximum value of the colormap range.
|
|
|
869 filename (str): The filename for saving the image.
|
|
|
870 """
|
|
|
871
|
|
|
872 # Create a colormap using matplotlib
|
|
|
873 cmap = plt.get_cmap(colorMap)
|
|
|
874
|
|
|
875 # Create a figure and axis
|
|
|
876 fig, ax = plt.subplots(figsize=(6, 1))
|
|
|
877 fig.subplots_adjust(bottom=0.5)
|
|
|
878
|
|
|
879 # Create a gradient image
|
|
|
880 gradient = np.linspace(0, 1, 256)
|
|
|
881 gradient = np.vstack((gradient, gradient))
|
|
|
882
|
|
|
883 # Add min and max value annotations
|
|
|
884 ax.text(0, 0.5, f'{np.round(min_value, 3)}', va='center', ha='right', transform=ax.transAxes, fontsize=12, color='black')
|
|
|
885 ax.text(1, 0.5, f'{np.round(max_value, 3)}', va='center', ha='left', transform=ax.transAxes, fontsize=12, color='black')
|
|
|
886
|
|
|
887
|
|
|
888 # Display the gradient image
|
|
|
889 ax.imshow(gradient, aspect='auto', cmap=cmap)
|
|
|
890 ax.set_axis_off()
|
|
|
891
|
|
|
892 # Save the image
|
|
|
893 plt.savefig(path.show(), bbox_inches='tight', pad_inches=0)
|
|
|
894 plt.close()
|
|
|
895 pass
|
|
|
896
|
|
|
897 def min_nonzero_abs(arr):
|
|
|
898 # Flatten the array and filter out zeros, then find the minimum of the remaining values
|
|
|
899 non_zero_elements = np.abs(arr)[np.abs(arr) > 0]
|
|
|
900 return np.min(non_zero_elements) if non_zero_elements.size > 0 else None
|
|
|
901
|
|
|
902 def computeEnrichmentMeanMedian(metabMap: ET.ElementTree, class_pat: Dict[str, List[List[float]]], ids: List[str], colormap:str) -> None:
|
|
|
903 """
|
|
|
904 Compute and visualize the metabolic map based on mean and median of the input fluxes.
|
|
168
|
905 The fluxes are normalised across classes/datasets and visualised using the given colormap.
|
|
4
|
906
|
|
|
907 Args:
|
|
|
908 metabMap (ET.ElementTree): An XML tree representing the metabolic map.
|
|
|
909 class_pat (Dict[str, List[List[float]]]): A dictionary where keys are class names and values are lists of enrichment values.
|
|
|
910 ids (List[str]): A list of reaction IDs to be used for coloring arrows.
|
|
|
911
|
|
|
912 Returns:
|
|
|
913 None
|
|
|
914 """
|
|
|
915 # Create copies only if they are needed
|
|
|
916 metabMap_mean = copy.deepcopy(metabMap)
|
|
|
917 metabMap_median = copy.deepcopy(metabMap)
|
|
|
918
|
|
|
919 # Compute medians and means
|
|
242
|
920 medians = {key: np.round(np.nanmedian(np.array(value), axis=1), 6) for key, value in class_pat.items()}
|
|
|
921 means = {key: np.round(np.nanmean(np.array(value), axis=1),6) for key, value in class_pat.items()}
|
|
4
|
922
|
|
|
923 # Normalize medians and means
|
|
|
924 max_flux_medians = max(np.max(np.abs(arr)) for arr in medians.values())
|
|
|
925 max_flux_means = max(np.max(np.abs(arr)) for arr in means.values())
|
|
|
926
|
|
168
|
927 min_flux_medians = min(min_nonzero_abs(arr) for arr in medians.values())
|
|
|
928 min_flux_means = min(min_nonzero_abs(arr) for arr in means.values())
|
|
4
|
929
|
|
168
|
930 medians = {key: median/max_flux_medians for key, median in medians.items()}
|
|
|
931 means = {key: mean/max_flux_means for key, mean in means.items()}
|
|
4
|
932
|
|
147
|
933 save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)
|
|
|
934 save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)
|
|
4
|
935
|
|
|
936 cmap = plt.get_cmap(colormap)
|
|
|
937
|
|
240
|
938 min_width = 2.0 # Minimum arrow width
|
|
|
939 max_width = 15.0 # Maximum arrow width
|
|
|
940
|
|
4
|
941 for key in class_pat:
|
|
|
942 # Create color mappings for median and mean
|
|
|
943 colors_median = {
|
|
168
|
944 rxn_id: rgb_to_hex(cmap(abs(medians[key][i]))) if medians[key][i] != 0 else '#bebebe' #grey blocked
|
|
4
|
945 for i, rxn_id in enumerate(ids)
|
|
|
946 }
|
|
|
947
|
|
|
948 colors_mean = {
|
|
168
|
949 rxn_id: rgb_to_hex(cmap(abs(means[key][i]))) if means[key][i] != 0 else '#bebebe' #grey blocked
|
|
4
|
950 for i, rxn_id in enumerate(ids)
|
|
|
951 }
|
|
|
952
|
|
|
953 for i, rxn_id in enumerate(ids):
|
|
240
|
954 # Calculate arrow width for median
|
|
|
955 width_median = np.interp(abs(medians[key][i]), [0, 1], [min_width, max_width])
|
|
4
|
956 isNegative = medians[key][i] < 0
|
|
240
|
957 apply_arrow(metabMap_median, rxn_id, colors_median[rxn_id], isNegative, width_median)
|
|
4
|
958
|
|
240
|
959 # Calculate arrow width for mean
|
|
|
960 width_mean = np.interp(abs(means[key][i]), [0, 1], [min_width, max_width])
|
|
4
|
961 isNegative = means[key][i] < 0
|
|
240
|
962 apply_arrow(metabMap_mean, rxn_id, colors_mean[rxn_id], isNegative, width_mean)
|
|
4
|
963
|
|
|
964 # Save and convert the SVG files
|
|
|
965 save_and_convert(metabMap_mean, "mean", key)
|
|
|
966 save_and_convert(metabMap_median, "median", key)
|
|
|
967
|
|
240
|
968 def apply_arrow(metabMap, rxn_id, color, isNegative, width=5):
|
|
4
|
969 """
|
|
|
970 Apply an arrow to a specific reaction in the metabolic map with a given color.
|
|
|
971
|
|
|
972 Args:
|
|
|
973 metabMap (ET.ElementTree): An XML tree representing the metabolic map.
|
|
|
974 rxn_id (str): The ID of the reaction to which the arrow will be applied.
|
|
|
975 color (str): The color of the arrow in hexadecimal format.
|
|
240
|
976 isNegative (bool): A boolean indicating if the arrow represents a negative value.
|
|
|
977 width (int): The width of the arrow.
|
|
4
|
978
|
|
|
979 Returns:
|
|
|
980 None
|
|
|
981 """
|
|
240
|
982 arrow = Arrow(width=width, col=color)
|
|
4
|
983 arrow.styleReactionElementsMeanMedian(metabMap, rxn_id, isNegative)
|
|
|
984 pass
|
|
|
985
|
|
|
986 def save_and_convert(metabMap, map_type, key):
|
|
|
987 """
|
|
|
988 Save the metabolic map as an SVG file and optionally convert it to PNG and PDF formats.
|
|
|
989
|
|
|
990 Args:
|
|
|
991 metabMap (ET.ElementTree): An XML tree representing the metabolic map.
|
|
|
992 map_type (str): The type of map ('mean' or 'median').
|
|
|
993 key (str): The key identifying the specific map.
|
|
|
994
|
|
|
995 Returns:
|
|
|
996 None
|
|
|
997 """
|
|
147
|
998 svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix=ARGS.output_path)
|
|
4
|
999 utils.writeSvg(svgFilePath, metabMap)
|
|
|
1000 if ARGS.generate_pdf:
|
|
147
|
1001 pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix=ARGS.output_path)
|
|
|
1002 pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix=ARGS.output_path)
|
|
4
|
1003 convert_to_pdf(svgFilePath, pngPath, pdfPath)
|
|
|
1004 if not ARGS.generate_svg:
|
|
|
1005 os.remove(svgFilePath.show())
|
|
|
1006
|
|
|
1007 ############################ MAIN #############################################
|
|
147
|
1008 def main(args:List[str] = None) -> None:
|
|
4
|
1009 """
|
|
|
1010 Initializes everything and sets the program in motion based on the fronted input arguments.
|
|
|
1011
|
|
|
1012 Returns:
|
|
|
1013 None
|
|
|
1014
|
|
|
1015 Raises:
|
|
|
1016 sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
|
|
|
1017 """
|
|
|
1018
|
|
|
1019 global ARGS
|
|
147
|
1020 ARGS = process_args(args)
|
|
4
|
1021
|
|
240
|
1022 if ARGS.custom_map == 'None':
|
|
|
1023 ARGS.custom_map = None
|
|
|
1024
|
|
147
|
1025 if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path)
|
|
4
|
1026
|
|
|
1027 core_map :ET.ElementTree = ARGS.choice_map.getMap(
|
|
|
1028 ARGS.tool_dir,
|
|
|
1029 utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
|
|
|
1030 # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.
|
|
|
1031 # getMap will None-check the customPath and panic when the model IS custom but there's no file (good). A cleaner
|
|
|
1032 # solution can be derived from my comment in FilePath.fromStrPath
|
|
|
1033
|
|
|
1034 ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas_fluxes, ARGS.input_data_fluxes, ARGS.input_class_fluxes, ARGS.names_fluxes)
|
|
|
1035
|
|
|
1036 if(ARGS.choice_map == utils.Model.HMRcore):
|
|
|
1037 temp_map = utils.Model.HMRcore_no_legend
|
|
|
1038 computeEnrichmentMeanMedian(temp_map.getMap(ARGS.tool_dir), class_pat, ids, ARGS.color_map)
|
|
|
1039 elif(ARGS.choice_map == utils.Model.ENGRO2):
|
|
|
1040 temp_map = utils.Model.ENGRO2_no_legend
|
|
|
1041 computeEnrichmentMeanMedian(temp_map.getMap(ARGS.tool_dir), class_pat, ids, ARGS.color_map)
|
|
|
1042 else:
|
|
|
1043 computeEnrichmentMeanMedian(core_map, class_pat, ids, ARGS.color_map)
|
|
148
|
1044
|
|
4
|
1045
|
|
151
|
1046 enrichment_results = computeEnrichment(class_pat, ids)
|
|
148
|
1047 for i, j, comparisonDict, max_z_score in enrichment_results:
|
|
|
1048 map_copy = copy.deepcopy(core_map)
|
|
|
1049 temp_thingsInCommon(comparisonDict, map_copy, max_z_score, i, j)
|
|
|
1050 createOutputMaps(i, j, map_copy)
|
|
4
|
1051
|
|
|
1052 if not ERRORS: return
|
|
|
1053 utils.logWarning(
|
|
|
1054 f"The following reaction IDs were mentioned in the dataset but weren't found in the map: {ERRORS}",
|
|
|
1055 ARGS.out_log)
|
|
|
1056
|
|
|
1057 print('Execution succeded')
|
|
|
1058
|
|
|
1059 ###############################################################################
|
|
|
1060 if __name__ == "__main__":
|
|
148
|
1061 main()
|
|
|
1062
|
