annotate utils/marea.py @ 285:b649d975c464 draft

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author luca_milaz
date Mon, 08 Jul 2024 22:59:05 +0000
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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 os
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13 import argparse
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14 import pyvips
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15 import utils.general_utils as utils
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16 from PIL import Image
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17 from typing import Tuple, Union, Optional, List, Dict
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18
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19 ERRORS = []
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20 ########################## argparse ##########################################
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21 ARGS :argparse.Namespace
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22 def process_args() -> argparse.Namespace:
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23 """
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24 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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25
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26 Args:
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27 args : Always obtained (in file) from sys.argv
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28
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29 Returns:
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30 Namespace : An object containing the parsed arguments
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31 """
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32 parser = argparse.ArgumentParser(
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33 usage = "%(prog)s [options]",
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34 description = "process some value's genes to create a comparison's map.")
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35
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36 #General:
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37 parser.add_argument(
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38 '-td', '--tool_dir',
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39 type = str,
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40 required = True,
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41 help = 'your tool directory')
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42
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43 parser.add_argument('-on', '--control', type = str)
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44 parser.add_argument('-ol', '--out_log', help = "Output log")
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45
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46 #Computation details:
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47 parser.add_argument(
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48 '-co', '--comparison',
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49 type = str,
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50 default = '1vs1',
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51 choices = ['manyvsmany', 'onevsrest', 'onevsmany'])
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52
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53 parser.add_argument(
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54 '-pv' ,'--pValue',
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55 type = float,
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56 default = 0.1,
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57 help = 'P-Value threshold (default: %(default)s)')
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58
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59 parser.add_argument(
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60 '-fc', '--fChange',
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61 type = float,
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62 default = 1.5,
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63 help = 'Fold-Change threshold (default: %(default)s)')
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64
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65 parser.add_argument(
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66 "-ne", "--net",
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67 type = utils.Bool("net"), default = False,
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68 help = "choose if you want net enrichment for RPS")
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69
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70 parser.add_argument(
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71 '-op', '--option',
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72 type = str,
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73 choices = ['datasets', 'dataset_class'],
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74 help='dataset or dataset and class')
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75
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76 #RAS:
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77 parser.add_argument(
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78 "-ra", "--using_RAS",
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79 type = utils.Bool("using_RAS"), default = True,
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80 help = "choose whether to use RAS datasets.")
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81
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82 parser.add_argument(
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83 '-id', '--input_data',
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84 type = str,
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85 help = 'input dataset')
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86
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87 parser.add_argument(
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88 '-ic', '--input_class',
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89 type = str,
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90 help = 'sample group specification')
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91
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92 parser.add_argument(
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93 '-ids', '--input_datas',
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94 type = str,
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95 nargs = '+',
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96 help = 'input datasets')
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97
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98 parser.add_argument(
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99 '-na', '--names',
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100 type = str,
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101 nargs = '+',
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102 help = 'input names')
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103
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104 #RPS:
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105 parser.add_argument(
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106 "-rp", "--using_RPS",
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107 type = utils.Bool("using_RPS"), default = False,
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108 help = "choose whether to use RPS datasets.")
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109
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110 parser.add_argument(
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111 '-idr', '--input_data_rps',
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112 type = str,
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113 help = 'input dataset rps')
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114
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115 parser.add_argument(
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116 '-icr', '--input_class_rps',
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117 type = str,
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118 help = 'sample group specification rps')
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119
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120 parser.add_argument(
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121 '-idsr', '--input_datas_rps',
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122 type = str,
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123 nargs = '+',
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124 help = 'input datasets rps')
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125
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126 parser.add_argument(
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127 '-nar', '--names_rps',
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128 type = str,
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129 nargs = '+',
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130 help = 'input names rps')
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131
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132 #Output:
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133 parser.add_argument(
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134 "-gs", "--generate_svg",
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135 type = utils.Bool("generate_svg"), default = True,
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136 help = "choose whether to use RAS datasets.")
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137
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138 parser.add_argument(
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139 "-gp", "--generate_pdf",
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140 type = utils.Bool("generate_pdf"), default = True,
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141 help = "choose whether to use RAS datasets.")
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142
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143 parser.add_argument(
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144 '-cm', '--custom_map',
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145 type = str,
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146 help='custom map to use')
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147
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148 parser.add_argument(
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149 '-mc', '--choice_map',
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150 type = utils.Model, default = utils.Model.HMRcore,
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151 choices = [utils.Model.HMRcore, utils.Model.ENGRO2, utils.Model.Custom])
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152
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153 args :argparse.Namespace = parser.parse_args()
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154 if args.using_RAS and not args.using_RPS: args.net = False
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155
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156 return args
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157
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158 ############################ dataset input ####################################
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159 def read_dataset(data :str, name :str) -> pd.DataFrame:
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160 """
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161 Tries to read the dataset from its path (data) as a tsv and turns it into a DataFrame.
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162
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163 Args:
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164 data : filepath of a dataset (from frontend input params or literals upon calling)
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165 name : name associated with the dataset (from frontend input params or literals upon calling)
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166
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167 Returns:
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168 pd.DataFrame : dataset in a runtime operable shape
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169
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170 Raises:
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171 sys.exit : if there's no data (pd.errors.EmptyDataError) or if the dataset has less than 2 columns
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172 """
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173 try:
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174 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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175 except pd.errors.EmptyDataError:
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176 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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177 if len(dataset.columns) < 2:
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178 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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179 return dataset
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180
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181 ############################ dataset name #####################################
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182 def name_dataset(name_data :str, count :int) -> str:
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183 """
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184 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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185
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186 Args:
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187 name_data : name associated with the dataset (from frontend input params)
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188 count : counter from 1 to make these names unique (external)
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189
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190 Returns:
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191 str : the name made unique
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192 """
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193 if str(name_data) == 'Dataset':
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194 return str(name_data) + '_' + str(count)
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195 else:
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196 return str(name_data)
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197
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198 ############################ map_methods ######################################
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199 FoldChange = Union[float, int, str] # Union[float, Literal[0, "-INF", "INF"]]
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200 def fold_change(avg1 :float, avg2 :float) -> FoldChange:
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201 """
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202 Calculates the fold change between two gene expression values.
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203
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204 Args:
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205 avg1 : average expression value from one dataset avg2 : average expression value from the other dataset
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206
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207 Returns:
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208 FoldChange :
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209 0 : when both input values are 0
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210 "-INF" : when avg1 is 0
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211 "INF" : when avg2 is 0
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212 float : for any other combination of values
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luca_milaz
parents:
diff changeset
213 """
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luca_milaz
parents:
diff changeset
214 if avg1 == 0 and avg2 == 0:
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luca_milaz
parents:
diff changeset
215 return 0
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luca_milaz
parents:
diff changeset
216 elif avg1 == 0:
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luca_milaz
parents:
diff changeset
217 return '-INF'
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luca_milaz
parents:
diff changeset
218 elif avg2 == 0:
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luca_milaz
parents:
diff changeset
219 return 'INF'
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luca_milaz
parents:
diff changeset
220 else:
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luca_milaz
parents:
diff changeset
221 return math.log(avg1 / avg2, 2)
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luca_milaz
parents:
diff changeset
222
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luca_milaz
parents:
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223 def fix_style(l :str, col :Optional[str], width :str, dash :str) -> str:
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luca_milaz
parents:
diff changeset
224 """
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luca_milaz
parents:
diff changeset
225 Produces a "fixed" style string to assign to a reaction arrow in the SVG map, assigning style properties to the corresponding values passed as input params.
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luca_milaz
parents:
diff changeset
226
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luca_milaz
parents:
diff changeset
227 Args:
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luca_milaz
parents:
diff changeset
228 l : current style string of an SVG element
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luca_milaz
parents:
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229 col : new value for the "stroke" style property
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luca_milaz
parents:
diff changeset
230 width : new value for the "stroke-width" style property
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luca_milaz
parents:
diff changeset
231 dash : new value for the "stroke-dasharray" style property
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luca_milaz
parents:
diff changeset
232
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luca_milaz
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233 Returns:
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luca_milaz
parents:
diff changeset
234 str : the fixed style string
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luca_milaz
parents:
diff changeset
235 """
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luca_milaz
parents:
diff changeset
236 tmp = l.split(';')
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luca_milaz
parents:
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237 flag_col = False
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luca_milaz
parents:
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238 flag_width = False
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luca_milaz
parents:
diff changeset
239 flag_dash = False
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luca_milaz
parents:
diff changeset
240 for i in range(len(tmp)):
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luca_milaz
parents:
diff changeset
241 if tmp[i].startswith('stroke:'):
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luca_milaz
parents:
diff changeset
242 tmp[i] = 'stroke:' + col
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luca_milaz
parents:
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243 flag_col = True
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luca_milaz
parents:
diff changeset
244 if tmp[i].startswith('stroke-width:'):
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luca_milaz
parents:
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245 tmp[i] = 'stroke-width:' + width
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luca_milaz
parents:
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246 flag_width = True
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luca_milaz
parents:
diff changeset
247 if tmp[i].startswith('stroke-dasharray:'):
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luca_milaz
parents:
diff changeset
248 tmp[i] = 'stroke-dasharray:' + dash
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luca_milaz
parents:
diff changeset
249 flag_dash = True
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luca_milaz
parents:
diff changeset
250 if not flag_col:
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luca_milaz
parents:
diff changeset
251 tmp.append('stroke:' + col)
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luca_milaz
parents:
diff changeset
252 if not flag_width:
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luca_milaz
parents:
diff changeset
253 tmp.append('stroke-width:' + width)
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luca_milaz
parents:
diff changeset
254 if not flag_dash:
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luca_milaz
parents:
diff changeset
255 tmp.append('stroke-dasharray:' + dash)
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luca_milaz
parents:
diff changeset
256 return ';'.join(tmp)
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luca_milaz
parents:
diff changeset
257
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luca_milaz
parents:
diff changeset
258 # The type of d values is collapsed, losing precision, because the dict containst lists instead of tuples, please fix!
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parents:
diff changeset
259 def fix_map(d :Dict[str, List[Union[float, FoldChange]]], core_map :ET.ElementTree, threshold_P_V :float, threshold_F_C :float, max_F_C :float) -> ET.ElementTree:
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luca_milaz
parents:
diff changeset
260 """
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luca_milaz
parents:
diff changeset
261 Edits the selected SVG map based on the p-value and fold change data (d) and some significance thresholds also passed as inputs.
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luca_milaz
parents:
diff changeset
262
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luca_milaz
parents:
diff changeset
263 Args:
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luca_milaz
parents:
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264 d : dictionary mapping a p-value and a fold-change value (values) to each reaction ID as encoded in the SVG map (keys)
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luca_milaz
parents:
diff changeset
265 core_map : SVG map to modify
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luca_milaz
parents:
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266 threshold_P_V : threshold for a p-value to be considered significant
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luca_milaz
parents:
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267 threshold_F_C : threshold for a fold change value to be considered significant
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luca_milaz
parents:
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268 max_F_C : highest fold change (absolute value)
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luca_milaz
parents:
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269
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luca_milaz
parents:
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270 Returns:
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luca_milaz
parents:
diff changeset
271 ET.ElementTree : the modified core_map
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luca_milaz
parents:
diff changeset
272
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luca_milaz
parents:
diff changeset
273 Side effects:
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luca_milaz
parents:
diff changeset
274 core_map : mut
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luca_milaz
parents:
diff changeset
275 """
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luca_milaz
parents:
diff changeset
276 maxT = 12
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luca_milaz
parents:
diff changeset
277 minT = 2
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luca_milaz
parents:
diff changeset
278 grey = '#BEBEBE'
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luca_milaz
parents:
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279 blue = '#0000FF'
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luca_milaz
parents:
diff changeset
280 red = '#E41A1C'
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luca_milaz
parents:
diff changeset
281 for el in core_map.iter():
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luca_milaz
parents:
diff changeset
282 el_id = str(el.get('id'))
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luca_milaz
parents:
diff changeset
283 if el_id.startswith('R_'):
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luca_milaz
parents:
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284 tmp = d.get(el_id[2:])
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luca_milaz
parents:
diff changeset
285 if tmp != None:
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luca_milaz
parents:
diff changeset
286 p_val :float = tmp[0]
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luca_milaz
parents:
diff changeset
287 f_c = tmp[1]
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luca_milaz
parents:
diff changeset
288 if p_val < threshold_P_V:
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luca_milaz
parents:
diff changeset
289 if not isinstance(f_c, str):
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luca_milaz
parents:
diff changeset
290 if abs(f_c) < math.log(threshold_F_C, 2):
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luca_milaz
parents:
diff changeset
291 col = grey
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luca_milaz
parents:
diff changeset
292 width = str(minT)
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luca_milaz
parents:
diff changeset
293 else:
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luca_milaz
parents:
diff changeset
294 if f_c < 0:
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luca_milaz
parents:
diff changeset
295 col = blue
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luca_milaz
parents:
diff changeset
296 elif f_c > 0:
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luca_milaz
parents:
diff changeset
297 col = red
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luca_milaz
parents:
diff changeset
298 width = str(max((abs(f_c) * maxT) / max_F_C, minT))
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luca_milaz
parents:
diff changeset
299 else:
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luca_milaz
parents:
diff changeset
300 if f_c == '-INF':
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luca_milaz
parents:
diff changeset
301 col = blue
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luca_milaz
parents:
diff changeset
302 elif f_c == 'INF':
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luca_milaz
parents:
diff changeset
303 col = red
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luca_milaz
parents:
diff changeset
304 width = str(maxT)
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luca_milaz
parents:
diff changeset
305 dash = 'none'
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luca_milaz
parents:
diff changeset
306 else:
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luca_milaz
parents:
diff changeset
307 dash = '5,5'
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luca_milaz
parents:
diff changeset
308 col = grey
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luca_milaz
parents:
diff changeset
309 width = str(minT)
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luca_milaz
parents:
diff changeset
310 el.set('style', fix_style(el.get('style', ""), col, width, dash))
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luca_milaz
parents:
diff changeset
311 return core_map
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luca_milaz
parents:
diff changeset
312
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luca_milaz
parents:
diff changeset
313 def getElementById(reactionId :str, metabMap :ET.ElementTree) -> utils.Result[ET.Element, utils.Result.ResultErr]:
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luca_milaz
parents:
diff changeset
314 """
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luca_milaz
parents:
diff changeset
315 Finds any element in the given map with the given ID. ID uniqueness in an svg file is recommended but
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luca_milaz
parents:
diff changeset
316 not enforced, if more than one element with the exact ID is found only the first will be returned.
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luca_milaz
parents:
diff changeset
317
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luca_milaz
parents:
diff changeset
318 Args:
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luca_milaz
parents:
diff changeset
319 reactionId (str): exact ID of the requested element.
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luca_milaz
parents:
diff changeset
320 metabMap (ET.ElementTree): metabolic map containing the element.
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luca_milaz
parents:
diff changeset
321
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luca_milaz
parents:
diff changeset
322 Returns:
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luca_milaz
parents:
diff changeset
323 utils.Result[ET.Element, ResultErr]: result of the search, either the first match found or a ResultErr.
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luca_milaz
parents:
diff changeset
324 """
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luca_milaz
parents:
diff changeset
325 return utils.Result.Ok(
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luca_milaz
parents:
diff changeset
326 f"//*[@id=\"{reactionId}\"]").map(
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luca_milaz
parents:
diff changeset
327 lambda xPath : metabMap.xpath(xPath)[0]).mapErr(
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luca_milaz
parents:
diff changeset
328 lambda _ : utils.Result.ResultErr(f"No elements with ID \"{reactionId}\" found in map"))
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luca_milaz
parents:
diff changeset
329 # ^^^ we shamelessly ignore the contents of the IndexError, it offers nothing to the user.
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luca_milaz
parents:
diff changeset
330
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luca_milaz
parents:
diff changeset
331 def styleMapElement(element :ET.Element, styleStr :str) -> None:
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luca_milaz
parents:
diff changeset
332 currentStyles :str = element.get("style", "")
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luca_milaz
parents:
diff changeset
333 if re.search(r";stroke:[^;]+;stroke-width:[^;]+;stroke-dasharray:[^;]+$", currentStyles):
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luca_milaz
parents:
diff changeset
334 currentStyles = ';'.join(currentStyles.split(';')[:-3])
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luca_milaz
parents:
diff changeset
335
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luca_milaz
parents:
diff changeset
336 element.set("style", currentStyles + styleStr)
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luca_milaz
parents:
diff changeset
337
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luca_milaz
parents:
diff changeset
338 class ReactionDirection(Enum):
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luca_milaz
parents:
diff changeset
339 Unknown = ""
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luca_milaz
parents:
diff changeset
340 Direct = "_F"
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luca_milaz
parents:
diff changeset
341 Inverse = "_B"
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luca_milaz
parents:
diff changeset
342
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luca_milaz
parents:
diff changeset
343 @classmethod
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luca_milaz
parents:
diff changeset
344 def fromDir(cls, s :str) -> "ReactionDirection":
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luca_milaz
parents:
diff changeset
345 # vvv as long as there's so few variants I actually condone the if spam:
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luca_milaz
parents:
diff changeset
346 if s == ReactionDirection.Direct.value: return ReactionDirection.Direct
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luca_milaz
parents:
diff changeset
347 if s == ReactionDirection.Inverse.value: return ReactionDirection.Inverse
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luca_milaz
parents:
diff changeset
348 return ReactionDirection.Unknown
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luca_milaz
parents:
diff changeset
349
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luca_milaz
parents:
diff changeset
350 @classmethod
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luca_milaz
parents:
diff changeset
351 def fromReactionId(cls, reactionId :str) -> "ReactionDirection":
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luca_milaz
parents:
diff changeset
352 return ReactionDirection.fromDir(reactionId[-2:])
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luca_milaz
parents:
diff changeset
353
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luca_milaz
parents:
diff changeset
354 def getArrowBodyElementId(reactionId :str) -> str:
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luca_milaz
parents:
diff changeset
355 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
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luca_milaz
parents:
diff changeset
356 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: reactionId = reactionId[:-2]
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luca_milaz
parents:
diff changeset
357 return f"R_{reactionId}"
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luca_milaz
parents:
diff changeset
358
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luca_milaz
parents:
diff changeset
359 def getArrowHeadElementId(reactionId :str) -> Tuple[str, str]:
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luca_milaz
parents:
diff changeset
360 """
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luca_milaz
parents:
diff changeset
361 We attempt extracting the direction information from the provided reaction ID, if unsuccessful we provide the IDs of both directions.
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luca_milaz
parents:
diff changeset
362
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luca_milaz
parents:
diff changeset
363 Args:
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luca_milaz
parents:
diff changeset
364 reactionId : the provided reaction ID.
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luca_milaz
parents:
diff changeset
365
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luca_milaz
parents:
diff changeset
366 Returns:
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luca_milaz
parents:
diff changeset
367 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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luca_milaz
parents:
diff changeset
368 """
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luca_milaz
parents:
diff changeset
369 if reactionId.endswith("_RV"): reactionId = reactionId[:-3] #TODO: standardize _RV
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luca_milaz
parents:
diff changeset
370 elif ReactionDirection.fromReactionId(reactionId) is not ReactionDirection.Unknown: return reactionId[:-3:-1] + reactionId[:-2], ""
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luca_milaz
parents:
diff changeset
371 return f"F_{reactionId}", f"B_{reactionId}"
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luca_milaz
parents:
diff changeset
372
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luca_milaz
parents:
diff changeset
373 class ArrowColor(Enum):
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luca_milaz
parents:
diff changeset
374 """
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luca_milaz
parents:
diff changeset
375 Encodes possible arrow colors based on their meaning in the enrichment process.
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luca_milaz
parents:
diff changeset
376 """
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luca_milaz
parents:
diff changeset
377 Invalid = "#BEBEBE" # gray, fold-change under treshold
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luca_milaz
parents:
diff changeset
378 UpRegulated = "#E41A1C" # red, up-regulated reaction
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luca_milaz
parents:
diff changeset
379 DownRegulated = "#0000FF" # blue, down-regulated reaction
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luca_milaz
parents:
diff changeset
380
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luca_milaz
parents:
diff changeset
381 UpRegulatedInv = "#FF7A00"
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luca_milaz
parents:
diff changeset
382 # ^^^ different shade of red (actually orange), up-regulated net value for a reversible reaction with
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luca_milaz
parents:
diff changeset
383 # conflicting enrichment in the two directions.
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luca_milaz
parents:
diff changeset
384
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luca_milaz
parents:
diff changeset
385 DownRegulatedInv = "#B22CF1"
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luca_milaz
parents:
diff changeset
386 # ^^^ different shade of blue (actually purple), down-regulated net value for a reversible reaction with
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luca_milaz
parents:
diff changeset
387 # conflicting enrichment in the two directions.
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luca_milaz
parents:
diff changeset
388
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luca_milaz
parents:
diff changeset
389 @classmethod
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luca_milaz
parents:
diff changeset
390 def fromFoldChangeSign(cls, foldChange :float, *, useAltColor = False) -> "ArrowColor":
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luca_milaz
parents:
diff changeset
391 colors = (cls.DownRegulated, cls.DownRegulatedInv) if foldChange < 0 else (cls.UpRegulated, cls.UpRegulatedInv)
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luca_milaz
parents:
diff changeset
392 return colors[useAltColor]
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luca_milaz
parents:
diff changeset
393
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luca_milaz
parents:
diff changeset
394 def __str__(self) -> str: return self.value
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luca_milaz
parents:
diff changeset
395
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luca_milaz
parents:
diff changeset
396 class Arrow:
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luca_milaz
parents:
diff changeset
397 """
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luca_milaz
parents:
diff changeset
398 Models the properties of a reaction arrow that change based on enrichment.
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luca_milaz
parents:
diff changeset
399 """
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luca_milaz
parents:
diff changeset
400 MIN_W = 2
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luca_milaz
parents:
diff changeset
401 MAX_W = 12
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luca_milaz
parents:
diff changeset
402
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luca_milaz
parents:
diff changeset
403 def __init__(self, width :int, col: ArrowColor, *, isDashed = False) -> None:
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luca_milaz
parents:
diff changeset
404 """
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luca_milaz
parents:
diff changeset
405 (Private) Initializes an instance of Arrow.
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luca_milaz
parents:
diff changeset
406
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luca_milaz
parents:
diff changeset
407 Args:
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luca_milaz
parents:
diff changeset
408 width : width of the arrow, ideally to be kept within Arrow.MIN_W and Arrow.MAX_W (not enforced).
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luca_milaz
parents:
diff changeset
409 col : color of the arrow.
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luca_milaz
parents:
diff changeset
410 isDashed : whether the arrow should be dashed, meaning the associated pValue resulted not significant.
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luca_milaz
parents:
diff changeset
411
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luca_milaz
parents:
diff changeset
412 Returns:
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luca_milaz
parents:
diff changeset
413 None : practically, a Arrow instance.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
414 """
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luca_milaz
parents:
diff changeset
415 self.w = width
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
416 self.col = col
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
417 self.dash = isDashed
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
418
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luca_milaz
parents:
diff changeset
419 def applyTo(self, reactionId :str, metabMap :ET.ElementTree, styleStr :str) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
420 if getElementById(reactionId, metabMap).map(lambda el : styleMapElement(el, styleStr)).isErr:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
421 ERRORS.append(reactionId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
422
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
423 def styleReactionElements(self, metabMap :ET.ElementTree, reactionId :str, *, mindReactionDir = True) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
424 # If We're dealing with RAS data or in general don't care about the direction of the reaction we only style the arrow body
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
425 if not mindReactionDir:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
426 return self.applyTo(getArrowBodyElementId(reactionId), metabMap, self.toStyleStr())
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
427
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
428 # Now we style the arrow head(s):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
429 idOpt1, idOpt2 = getArrowHeadElementId(reactionId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
430 self.applyTo(idOpt1, metabMap, self.toStyleStr(downSizedForTips = True))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
431 if idOpt2: self.applyTo(idOpt2, metabMap, self.toStyleStr(downSizedForTips = True))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
432
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
433 def getMapReactionId(self, reactionId :str, mindReactionDir :bool) -> str:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
434 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
435 Computes the reaction ID as encoded in the map for a given reaction ID from the dataset.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
436
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
437 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
438 reactionId: the reaction ID, as encoded in the dataset.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
439 mindReactionDir: if True forward (F_) and backward (B_) directions will be encoded in the result.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
440
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
441 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
442 str : the ID of an arrow's body or tips in the map.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
443 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
444 # we assume the reactionIds also don't encode reaction dir if they don't mind it when styling the map.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
445 if not mindReactionDir: return "R_" + reactionId
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
446
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
447 #TODO: this is clearly something we need to make consistent in RPS
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
448 return (reactionId[:-3:-1] + reactionId[:-2]) if reactionId[:-2] in ["_F", "_B"] else f"F_{reactionId}" # "Pyr_F" --> "F_Pyr"
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
449
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
450 def toStyleStr(self, *, downSizedForTips = False) -> str:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
451 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
452 Collapses the styles of this Arrow into a str, ready to be applied as part of the "style" property on an svg element.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
453
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
454 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
455 str : the styles string.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
456 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
457 width = self.w
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
458 if downSizedForTips: width *= 0.15
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
459 return f";stroke:{self.col};stroke-width:{width};stroke-dasharray:{'5,5' if self.dash else 'none'}"
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
460
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
461 # vvv These constants could be inside the class itself a static properties, but python
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
462 # was built by brainless organisms so here we are!
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luca_milaz
parents:
diff changeset
463 INVALID_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
464 INSIGNIFICANT_ARROW = Arrow(Arrow.MIN_W, ArrowColor.Invalid, isDashed = True)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
465
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luca_milaz
parents:
diff changeset
466 def applyRpsEnrichmentToMap(rpsEnrichmentRes :Dict[str, Union[Tuple[float, FoldChange], Tuple[float, FoldChange, float, float]]], metabMap :ET.ElementTree, maxNumericFoldChange :float) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
467 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
468 Applies RPS enrichment results to the provided metabolic map.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
469
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
470 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
471 rpsEnrichmentRes : RPS enrichment results.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
472 metabMap : the metabolic map to edit.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
473 maxNumericFoldChange : biggest finite fold-change value found.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
474
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
475 Side effects:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
476 metabMap : mut
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
477
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
478 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
479 None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
480 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
481 for reactionId, values in rpsEnrichmentRes.items():
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
482 pValue = values[0]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
483 foldChange = values[1]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
484
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
485 if isinstance(foldChange, str): foldChange = float(foldChange)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
486 if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
487 INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
488 continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
489
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
490 if abs(foldChange) < math.log(ARGS.fChange, 2):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
491 INVALID_ARROW.styleReactionElements(metabMap, reactionId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
492 continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
493
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
494 width = Arrow.MAX_W
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
495 if not math.isinf(foldChange):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
496 try: width = max(abs(foldChange * Arrow.MAX_W) / maxNumericFoldChange, Arrow.MIN_W)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
497 except ZeroDivisionError: pass
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
498
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
499 if not reactionId.endswith("_RV"): # RV stands for reversible reactions
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
500 Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
501 continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
502
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
503 reactionId = reactionId[:-3] # Remove "_RV"
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
504
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
505 inversionScore = (values[2] < 0) + (values[3] < 0) # Compacts the signs of averages into 1 easy to check score
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
506 if inversionScore == 2: foldChange *= -1
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
507 # ^^^ Style the inverse direction with the opposite sign netValue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
508
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
509 # If the score is 1 (opposite signs) we use alternative colors vvv
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
510 arrow = Arrow(width, ArrowColor.fromFoldChangeSign(foldChange, useAltColor = inversionScore == 1))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
511
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
512 # vvv These 2 if statements can both be true and can both happen
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
513 if ARGS.net: # style arrow head(s):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
514 arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
515
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
516 if not ARGS.using_RAS: # style arrow body
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
517 arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
518
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
519 ############################ split class ######################################
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
520 def split_class(classes :pd.DataFrame, resolve_rules :Dict[str, List[float]]) -> Dict[str, List[List[float]]]:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
521 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
522 Generates a :dict that groups together data from a :DataFrame based on classes the data is related to.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
523
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
524 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
525 classes : a :DataFrame of only string values, containing class information (rows) and keys to query the resolve_rules :dict
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
526 resolve_rules : a :dict containing :float data
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
527
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
528 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
529 dict : the dict with data grouped by class
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
530
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
531 Side effects:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
532 classes : mut
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
533 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
534 class_pat :Dict[str, List[List[float]]] = {}
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
535 for i in range(len(classes)):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
536 classe :str = classes.iloc[i, 1]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
537 if pd.isnull(classe): continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
538
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
539 l :List[List[float]] = []
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
540 for j in range(i, len(classes)):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
541 if classes.iloc[j, 1] == classe:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
542 pat_id :str = classes.iloc[j, 0]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
543 tmp = resolve_rules.get(pat_id, None)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
544 if tmp != None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
545 l.append(tmp)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
546 classes.iloc[j, 1] = None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
547
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
548 if l:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
549 class_pat[classe] = list(map(list, zip(*l)))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
550 continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
551
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
552 utils.logWarning(
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
553 f"Warning: no sample found in class \"{classe}\", the class has been disregarded", ARGS.out_log)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
554
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
555 return class_pat
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
556
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
557 ############################ conversion ##############################################
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
558 #conversion from svg to png
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
559 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:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
560 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
561 Internal utility to convert an SVG to PNG (forced opaque) to aid in PDF conversion.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
562
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
563 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
564 svg_path : path to SVG file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
565 png_path : path for new PNG file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
566 dpi : dots per inch of the generated PNG
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
567 scale : scaling factor for the generated PNG, computed internally when a size is provided
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
568 size : final effective width of the generated PNG
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
569
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
570 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
571 None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
572 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
573 if size:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
574 image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=1)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
575 scale = size / image.width
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
576 image = image.resize(scale)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
577 else:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
578 image = pyvips.Image.new_from_file(svg_path.show(), dpi=dpi, scale=scale)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
579
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
580 white_background = pyvips.Image.black(image.width, image.height).new_from_image([255, 255, 255])
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
581 white_background = white_background.affine([scale, 0, 0, scale])
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
582
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
583 if white_background.bands != image.bands:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
584 white_background = white_background.extract_band(0)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
585
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
586 composite_image = white_background.composite2(image, 'over')
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
587 composite_image.write_to_file(png_path.show())
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
588
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
589 #funzione unica, lascio fuori i file e li passo in input
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
590 #conversion from png to pdf
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
591 def convert_png_to_pdf(png_file :utils.FilePath, pdf_file :utils.FilePath) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
592 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
593 Internal utility to convert a PNG to PDF to aid from SVG conversion.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
594
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
595 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
596 png_file : path to PNG file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
597 pdf_file : path to new PDF file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
598
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
599 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
600 None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
601 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
602 image = Image.open(png_file.show())
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
603 image = image.convert("RGB")
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
604 image.save(pdf_file.show(), "PDF", resolution=100.0)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
605
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
606 #function called to reduce redundancy in the code
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
607 def convert_to_pdf(file_svg :utils.FilePath, file_png :utils.FilePath, file_pdf :utils.FilePath) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
608 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
609 Converts the SVG map at the provided path to PDF.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
610
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
611 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
612 file_svg : path to SVG file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
613 file_png : path to PNG file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
614 file_pdf : path to new PDF file
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
615
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
616 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
617 None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
618 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
619 svg_to_png_with_background(file_svg, file_png)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
620 try:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
621 convert_png_to_pdf(file_png, file_pdf)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
622 print(f'PDF file {file_pdf.filePath} successfully generated.')
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
623
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
624 except Exception as e:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
625 raise utils.DataErr(file_pdf.show(), f'Error generating PDF file: {e}')
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
626
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
627 ############################ map ##############################################
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luca_milaz
parents:
diff changeset
628 def buildOutputPath(dataset1Name :str, dataset2Name = "rest", *, details = "", ext :utils.FileFormat) -> utils.FilePath:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
629 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
630 Builds a FilePath instance from the names of confronted datasets ready to point to a location in the
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
631 "result/" folder, used by this tool for output files in collections.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
632
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
633 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
634 dataset1Name : _description_
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
635 dataset2Name : _description_. Defaults to "rest".
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
636 details : _description_
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
637 ext : _description_
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
638
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
639 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
640 utils.FilePath : _description_
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
641 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
642 # This function returns a util data structure but is extremely specific to this module.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
643 # RAS also uses collections as output and as such might benefit from a method like this, but I'd wait
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
644 # TODO: until a third tool with multiple outputs appears before porting this to utils.
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luca_milaz
parents:
diff changeset
645 return utils.FilePath(
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
646 f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
647 # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
648 # all output files: I don't care, this was never the performance bottleneck of the tool and
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
649 # there is no other net gain in saving and re-using the built string.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
650 ext,
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
651 prefix = "result")
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
652
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
653 FIELD_NOT_AVAILABLE = '/'
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
654 def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
655 fieldsAmt = len(fieldNames)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
656 with open(outPath.show(), "w", newline = "") as fd:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
657 writer = csv.DictWriter(fd, fieldnames = fieldNames, delimiter = '\t')
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
658 writer.writeheader()
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
659
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
660 for row in rows:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
661 sizeMismatch = fieldsAmt - len(row)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
662 if sizeMismatch > 0: row.extend([FIELD_NOT_AVAILABLE] * sizeMismatch)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
663 writer.writerow({ field : data for field, data in zip(fieldNames, row) })
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
664
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
665 OldEnrichedScores = Dict[str, List[Union[float, FoldChange]]] #TODO: try to use Tuple whenever possible
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
666 def writeTabularResult(enrichedScores : OldEnrichedScores, ras_enrichment: bool, outPath :utils.FilePath) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
667 fieldNames = ["ids", "P_Value", "Log2(fold change)"]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
668 if not ras_enrichment: fieldNames.extend(["average_1", "average_2"])
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
669
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
670 writeToCsv([ [reactId] + values for reactId, values in enrichedScores.items() ], fieldNames, outPath)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
671
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
672 def temp_thingsInCommon(tmp :Dict[str, List[Union[float, FoldChange]]], core_map :ET.ElementTree, max_F_C :float, dataset1Name :str, dataset2Name = "rest", ras_enrichment = True) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
673 # this function compiles the things always in common between comparison modes after enrichment.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
674 # TODO: organize, name better.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
675 writeTabularResult(tmp, ras_enrichment, buildOutputPath(dataset1Name, dataset2Name, details = "Tabular Result", ext = utils.FileFormat.TSV))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
676
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
677 if ras_enrichment:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
678 fix_map(tmp, core_map, ARGS.pValue, ARGS.fChange, max_F_C)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
679 return
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
680
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
681 for reactId, enrichData in tmp.items(): tmp[reactId] = tuple(enrichData)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
682 applyRpsEnrichmentToMap(tmp, core_map, max_F_C)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
683
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
684 def computePValue(dataset1Data :List[float], dataset2Data :List[float]) -> float:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
685 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
686 Computes the statistical significance score (P-value) of the comparison between coherent data
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
687 from two datasets. The data is supposed to, in both datasets:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
688 - be related to the same reaction ID;
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
689 - be ordered by sample, such that the item at position i in both lists is related to the
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
690 same sample or cell line.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
691
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
692 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
693 dataset1Data : data from the 1st dataset.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
694 dataset2Data : data from the 2nd dataset.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
695
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
696 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
697 float: P-value from a Kolmogorov-Smirnov test on the provided data.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
698 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
699 return st.ks_2samp(dataset1Data, dataset2Data)[1]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
700
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
701 def compareDatasetPair(dataset1Data :List[List[float]], dataset2Data :List[List[float]], ids :List[str]) -> Tuple[Dict[str, List[Union[float, FoldChange]]], float]:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
702 #TODO: the following code still suffers from "dumbvarnames-osis"
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
703 tmp :Dict[str, List[Union[float, FoldChange]]] = {}
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
704 count = 0
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
705 max_F_C = 0
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
706
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
707 for l1, l2 in zip(dataset1Data, dataset2Data):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
708 reactId = ids[count]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
709 count += 1
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
710 if not reactId: continue # we skip ids that have already been processed
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
711
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
712 try: #TODO: identify the source of these errors and minimize code in the try block
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
713 reactDir = ReactionDirection.fromReactionId(reactId)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
714 # Net score is computed only for reversible reactions when user wants it on arrow tips or when RAS datasets aren't used
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
715 if (ARGS.net or not ARGS.using_RAS) and reactDir is not ReactionDirection.Unknown:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
716 try: position = ids.index(reactId[:-1] + ('B' if reactDir is ReactionDirection.Direct else 'F'))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
717 except ValueError: continue # we look for the complementary id, if not found we skip
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
718
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
719 nets1 = np.subtract(l1, dataset1Data[position])
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
720 nets2 = np.subtract(l2, dataset2Data[position])
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
721
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
722 p_value = computePValue(nets1, nets2)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
723 avg1 = sum(nets1) / len(nets1)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
724 avg2 = sum(nets2) / len(nets2)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
725 net = (avg1 - avg2) / abs(avg2)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
726
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
727 if math.isnan(net): continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
728 tmp[reactId[:-1] + "RV"] = [p_value, net, avg1, avg2]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
729
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
730 # vvv complementary directional ids are set to None once processed if net is to be applied to tips
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
731 if ARGS.net:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
732 ids[position] = None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
733 continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
734
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
735 # fallthrough is intended, regular scores need to be computed when tips aren't net but RAS datasets aren't used
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
736 p_value = computePValue(l1, l2)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
737 avg = fold_change(sum(l1) / len(l1), sum(l2) / len(l2))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
738 if not isinstance(avg, str) and max_F_C < abs(avg): max_F_C = abs(avg)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
739 tmp[reactId] = [float(p_value), avg]
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
740
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
741 except (TypeError, ZeroDivisionError): continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
742
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
743 return tmp, max_F_C
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
744
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
745 def computeEnrichment(metabMap :ET.ElementTree, class_pat :Dict[str, List[List[float]]], ids :List[str], *, fromRAS = True) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
746 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
747 Compares clustered data based on a given comparison mode and applies enrichment-based styling on the
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
748 provided metabolic map.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
749
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
750 Args:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
751 metabMap : SVG map to modify.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
752 class_pat : the clustered data.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
753 ids : ids for data association.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
754 fromRAS : whether the data to enrich consists of RAS scores.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
755
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
756 Returns:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
757 None
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
758
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
759 Raises:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
760 sys.exit : if there are less than 2 classes for comparison
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
761
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
762 Side effects:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
763 metabMap : mut
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
764 ids : mut
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
765 """
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
766 class_pat = { k.strip() : v for k, v in class_pat.items() }
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
767 #TODO: simplfy this stuff vvv and stop using sys.exit (raise the correct utils error)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
768 if (not class_pat) or (len(class_pat.keys()) < 2): sys.exit('Execution aborted: classes provided for comparisons are less than two\n')
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
769
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
770 if ARGS.comparison == "manyvsmany":
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
771 for i, j in it.combinations(class_pat.keys(), 2):
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
772 #TODO: these 2 functions are always called in pair and in this order and need common data,
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
773 # some clever refactoring would be appreciated.
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
774 comparisonDict, max_F_C = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
775 temp_thingsInCommon(comparisonDict, metabMap, max_F_C, i, j, fromRAS)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
776
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
777 elif ARGS.comparison == "onevsrest":
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
778 for single_cluster in class_pat.keys():
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
779 t :List[List[List[float]]] = []
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
780 for k in class_pat.keys():
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
781 if k != single_cluster:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
782 t.append(class_pat.get(k))
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
783
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
784 rest :List[List[float]] = []
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
785 for i in t:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
786 rest = rest + i
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
787
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
788 comparisonDict, max_F_C = compareDatasetPair(class_pat.get(single_cluster), rest, ids)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
789 temp_thingsInCommon(comparisonDict, metabMap, max_F_C, single_cluster, fromRAS)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
790
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
791 elif ARGS.comparison == "onevsmany":
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
792 controlItems = class_pat.get(ARGS.control)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
793 for otherDataset in class_pat.keys():
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
794 if otherDataset == ARGS.control: continue
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
795
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
796 comparisonDict, max_F_C = compareDatasetPair(controlItems, class_pat.get(otherDataset), ids)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
797 temp_thingsInCommon(comparisonDict, metabMap, max_F_C, ARGS.control, otherDataset, fromRAS)
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
798
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
799 def createOutputMaps(dataset1Name :str, dataset2Name :str, core_map :ET.ElementTree) -> None:
b649d975c464 Uploaded
luca_milaz
parents:
diff changeset
800 svgFilePath = buildOutputPath(dataset1Name, dataset2Name, details = "SVG Map", ext = utils.FileFormat.SVG)
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diff changeset
801 utils.writeSvg(svgFilePath, core_map)
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802
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diff changeset
803 if ARGS.generate_pdf:
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diff changeset
804 pngPath = buildOutputPath(dataset1Name, dataset2Name, details = "PNG Map", ext = utils.FileFormat.PNG)
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diff changeset
805 pdfPath = buildOutputPath(dataset1Name, dataset2Name, details = "PDF Map", ext = utils.FileFormat.PDF)
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diff changeset
806 convert_to_pdf(svgFilePath, pngPath, pdfPath)
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diff changeset
807
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diff changeset
808 if not ARGS.generate_svg: os.remove(svgFilePath.show())
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diff changeset
809
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diff changeset
810 ClassPat = Dict[str, List[List[float]]]
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811 def getClassesAndIdsFromDatasets(datasetsPaths :List[str], datasetPath :str, classPath :str, names :List[str]) -> Tuple[List[str], ClassPat]:
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812 # TODO: I suggest creating dicts with ids as keys instead of keeping class_pat and ids separate,
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diff changeset
813 # for the sake of everyone's sanity.
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diff changeset
814 class_pat :ClassPat = {}
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815 if ARGS.option == 'datasets':
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diff changeset
816 num = 1 #TODO: the dataset naming function could be a generator
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817 for path, name in zip(datasetsPaths, names):
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818 name = name_dataset(name, num)
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diff changeset
819 resolve_rules_float, ids = getDatasetValues(path, name)
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820 if resolve_rules_float != None:
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821 class_pat[name] = list(map(list, zip(*resolve_rules_float.values())))
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822
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diff changeset
823 num += 1
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diff changeset
824
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825 elif ARGS.option == "dataset_class":
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diff changeset
826 classes = read_dataset(classPath, "class")
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827 classes = classes.astype(str)
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diff changeset
828
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diff changeset
829 resolve_rules_float, ids = getDatasetValues(datasetPath, "Dataset Class (not actual name)")
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diff changeset
830 if resolve_rules_float != None: class_pat = split_class(classes, resolve_rules_float)
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831
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diff changeset
832 return ids, class_pat
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diff changeset
833 #^^^ 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)
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diff changeset
834
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diff changeset
835 #TODO: create these damn args as FilePath objects
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diff changeset
836 def getDatasetValues(datasetPath :str, datasetName :str) -> Tuple[ClassPat, List[str]]:
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diff changeset
837 """
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diff changeset
838 Opens the dataset at the given path and extracts the values (expected nullable numerics) and the IDs.
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diff changeset
839
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840 Args:
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diff changeset
841 datasetPath : path to the dataset
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diff changeset
842 datasetName (str): dataset name, used in error reporting
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diff changeset
843
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diff changeset
844 Returns:
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diff changeset
845 Tuple[ClassPat, List[str]]: values and IDs extracted from the dataset
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846 """
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parents:
diff changeset
847 dataset = read_dataset(datasetPath, datasetName)
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diff changeset
848 IDs = pd.Series.tolist(dataset.iloc[:, 0].astype(str))
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849
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diff changeset
850 dataset = dataset.drop(dataset.columns[0], axis = "columns").to_dict("list")
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diff changeset
851 return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs
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diff changeset
852
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diff changeset
853 ############################ MAIN #############################################
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luca_milaz
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diff changeset
854 def main() -> None:
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luca_milaz
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diff changeset
855 """
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luca_milaz
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diff changeset
856 Initializes everything and sets the program in motion based on the fronted input arguments.
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luca_milaz
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diff changeset
857
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858 Returns:
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diff changeset
859 None
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luca_milaz
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diff changeset
860
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luca_milaz
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diff changeset
861 Raises:
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luca_milaz
parents:
diff changeset
862 sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
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luca_milaz
parents:
diff changeset
863 """
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luca_milaz
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diff changeset
864 global ARGS
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luca_milaz
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diff changeset
865 ARGS = process_args()
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luca_milaz
parents:
diff changeset
866
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luca_milaz
parents:
diff changeset
867 if os.path.isdir('result') == False: os.makedirs('result')
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luca_milaz
parents:
diff changeset
868
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diff changeset
869 core_map :ET.ElementTree = ARGS.choice_map.getMap(
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parents:
diff changeset
870 ARGS.tool_dir,
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luca_milaz
parents:
diff changeset
871 utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
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luca_milaz
parents:
diff changeset
872 # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.
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luca_milaz
parents:
diff changeset
873 # getMap will None-check the customPath and panic when the model IS custom but there's no file (good). A cleaner
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luca_milaz
parents:
diff changeset
874 # solution can be derived from my comment in FilePath.fromStrPath
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luca_milaz
parents:
diff changeset
875
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luca_milaz
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diff changeset
876 if ARGS.using_RAS:
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luca_milaz
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diff changeset
877 ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas, ARGS.input_data, ARGS.input_class, ARGS.names)
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luca_milaz
parents:
diff changeset
878 computeEnrichment(core_map, class_pat, ids)
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luca_milaz
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diff changeset
879
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luca_milaz
parents:
diff changeset
880 if ARGS.using_RPS:
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luca_milaz
parents:
diff changeset
881 ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas_rps, ARGS.input_data_rps, ARGS.input_class_rps, ARGS.names_rps)
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parents:
diff changeset
882 computeEnrichment(core_map, class_pat, ids, fromRAS = False)
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luca_milaz
parents:
diff changeset
883
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luca_milaz
parents:
diff changeset
884 # create output files: TODO: this is the same comparison happening in "maps", find a better way to organize this
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luca_milaz
parents:
diff changeset
885 if ARGS.comparison == "manyvsmany":
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luca_milaz
parents:
diff changeset
886 for i, j in it.combinations(class_pat.keys(), 2): createOutputMaps(i, j, core_map)
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luca_milaz
parents:
diff changeset
887 return
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luca_milaz
parents:
diff changeset
888
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luca_milaz
parents:
diff changeset
889 if ARGS.comparison == "onevsrest":
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luca_milaz
parents:
diff changeset
890 for single_cluster in class_pat.keys(): createOutputMaps(single_cluster, "rest", core_map)
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luca_milaz
parents:
diff changeset
891 return
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parents:
diff changeset
892
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luca_milaz
parents:
diff changeset
893 for otherDataset in class_pat.keys():
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luca_milaz
parents:
diff changeset
894 if otherDataset != ARGS.control: createOutputMaps(i, j, core_map)
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luca_milaz
parents:
diff changeset
895
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luca_milaz
parents:
diff changeset
896 if not ERRORS: return
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luca_milaz
parents:
diff changeset
897 utils.logWarning(
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luca_milaz
parents:
diff changeset
898 f"The following reaction IDs were mentioned in the dataset but weren't found in the map: {ERRORS}",
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luca_milaz
parents:
diff changeset
899 ARGS.out_log)
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luca_milaz
parents:
diff changeset
900
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luca_milaz
parents:
diff changeset
901 print('Execution succeded')
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luca_milaz
parents:
diff changeset
902
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luca_milaz
parents:
diff changeset
903 ###############################################################################
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luca_milaz
parents:
diff changeset
904 if __name__ == "__main__":
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luca_milaz
parents:
diff changeset
905 main()