Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 185:c933b2c6a39e draft

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Uploaded
author francesco_lapi
date Wed, 20 Nov 2024 17:27:41 +0000
parents fa981714e87d
children f0197057876c
comparison
equal deleted inserted replaced
184:b5b7960a208e 185:c933b2c6a39e
125 type = str, 125 type = str,
126 default='result', 126 default='result',
127 help = 'output path for maps') 127 help = 'output path for maps')
128 128
129 args :argparse.Namespace = parser.parse_args(args) 129 args :argparse.Namespace = parser.parse_args(args)
130 args.net = True 130 args.net = True # TODO SICCOME I FLUSSI POSSONO ESSERE ANCHE NEGATIVI SONO SEMPRE CONSIDERATI NETTI
131 131
132 return args 132 return args
133 133
134 ############################ dataset input #################################### 134 ############################ dataset input ####################################
135 def read_dataset(data :str, name :str) -> pd.DataFrame: 135 def read_dataset(data :str, name :str) -> pd.DataFrame:
250 core_map : mut 250 core_map : mut
251 """ 251 """
252 maxT = 12 252 maxT = 12
253 minT = 2 253 minT = 2
254 grey = '#BEBEBE' 254 grey = '#BEBEBE'
255 blue = '#6495ed' 255 blue = '#6495ed' # azzurrino
256 red = '#ecac68' 256 red = '#ecac68' # arancione
257 for el in core_map.iter(): 257 for el in core_map.iter():
258 el_id = str(el.get('id')) 258 el_id = str(el.get('id'))
259 if el_id.startswith('R_'): 259 if el_id.startswith('R_'):
260 tmp = d.get(el_id[2:]) 260 tmp = d.get(el_id[2:])
261 if tmp != None: 261 if tmp != None:
493 if not math.isinf(foldChange): 493 if not math.isinf(foldChange):
494 try: 494 try:
495 width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W) 495 width = max(abs(z_score * Arrow.MAX_W) / maxNumericZScore, Arrow.MIN_W)
496 496
497 except ZeroDivisionError: pass 497 except ZeroDivisionError: pass
498 498 # TODO CHECK RV
499 #if not reactionId.endswith("_RV"): # RV stands for reversible reactions 499 #if not reactionId.endswith("_RV"): # RV stands for reversible reactions
500 # Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId) 500 # Arrow(width, ArrowColor.fromFoldChangeSign(foldChange)).styleReactionElements(metabMap, reactionId)
501 # continue 501 # continue
502 502
503 #reactionId = reactionId[:-3] # Remove "_RV" 503 #reactionId = reactionId[:-3] # Remove "_RV"
512 # vvv These 2 if statements can both be true and can both happen 512 # vvv These 2 if statements can both be true and can both happen
513 if ARGS.net: # style arrow head(s): 513 if ARGS.net: # style arrow head(s):
514 arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F")) 514 arrow.styleReactionElements(metabMap, reactionId + ("_B" if inversionScore == 2 else "_F"))
515 arrow.applyTo(("F_" if inversionScore == 2 else "B_") + reactionId, metabMap, f";stroke:{ArrowColor.Transparent};stroke-width:0;stroke-dasharray:None") 515 arrow.applyTo(("F_" if inversionScore == 2 else "B_") + reactionId, metabMap, f";stroke:{ArrowColor.Transparent};stroke-width:0;stroke-dasharray:None")
516 516
517 arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = False) 517 arrow.styleReactionElements(metabMap, reactionId, mindReactionDir = True)
518 518
519 519
520 ############################ split class ###################################### 520 ############################ split class ######################################
521 def split_class(classes :pd.DataFrame, resolve_rules :Dict[str, List[float]]) -> Dict[str, List[List[float]]]: 521 def split_class(classes :pd.DataFrame, resolve_rules :Dict[str, List[float]]) -> Dict[str, List[List[float]]]:
522 """ 522 """