From 22a72417684400b6d4754d2eb60be7f5b9a0320c Mon Sep 17 00:00:00 2001
From: local_comparaison <mathieu.umec@inrae.fr>
Date: Mon, 15 Jan 2024 14:53:24 +0100
Subject: [PATCH] adjust for CPDB visu
---
Visualisation_des_donnes_de_mapping.py | 9 +--
complete_processing_of_mapping_results.py | 71 ++++++++++++++++-------
2 files changed, 55 insertions(+), 25 deletions(-)
diff --git a/Visualisation_des_donnes_de_mapping.py b/Visualisation_des_donnes_de_mapping.py
index 769b37f..cd041bd 100644
--- a/Visualisation_des_donnes_de_mapping.py
+++ b/Visualisation_des_donnes_de_mapping.py
@@ -138,7 +138,7 @@ def up_down_path_plot(l_path, up, down, log_p):
return : 1 plot of regulation pathways
"""
- fig, ax1 = plt.subplots()
+ fig, ax1 = plt.subplots(figsize=(22, 14))
plt.subplots_adjust(top=0.95, bottom=0.30)
l_bar = 0.8
x = range(len(down))
@@ -152,10 +152,10 @@ def up_down_path_plot(l_path, up, down, log_p):
ax2.set_xlabel("Pathways")
ax2.set_ylabel("-log(pvalue)")
plt.ylim(bottom = 0, top=max(log_p)+0.5)
- fig.legend(loc='upper right', bbox_to_anchor=(0.9, 0.88))
+ fig.legend(loc='upper right', bbox_to_anchor=(0.9, 0.95))
ax1.set_xticks(l_path)
ax1.set_xticklabels(l_path, size=6.5, rotation=-90, ha='center')
- plt.show()
+ return(fig)
if __name__ == "__main__":
@@ -163,7 +163,8 @@ if __name__ == "__main__":
UP = [5, 8, 21]
DOWN = [41, 13, 9]
LOG_P = [13.61, 7.96, 4.64]
- up_down_path_plot(L_PATH, UP, DOWN, LOG_P)
+ figg = up_down_path_plot(L_PATH, UP, DOWN, LOG_P)
+ plt.show()
diff --git a/complete_processing_of_mapping_results.py b/complete_processing_of_mapping_results.py
index 2c45122..8c30fde 100644
--- a/complete_processing_of_mapping_results.py
+++ b/complete_processing_of_mapping_results.py
@@ -8,7 +8,7 @@ import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
-from math import log
+from math import log, floor
import sys
sys.path.append('C:\\Users\\mumec\\Desktop\\Dossier_gitlab_local\\traitement_des_données')
from Visualisation_des_donnes_de_mapping import up_down_path_plot
@@ -91,6 +91,9 @@ def recup_ramp_pathways_list(ramp_mapping_result, correspondence_file):
return l_to_return
+def recup_ramp_enrichment_pathways_list(ramp_mapping_result, correspondence_file):
+
+
def recup_cpdb_pathways_list(cpdb_mapping_result, correspondence_file):
"""
Give a list of pathways with the correspondent metabolites names
@@ -108,6 +111,8 @@ def recup_cpdb_pathways_list(cpdb_mapping_result, correspondence_file):
l_pathways = l_pathways[1:]
l_path_metabo_whith_top = column_recovery(cpdb_mapping_result, 5)
l_path_metabo = l_path_metabo_whith_top[1:]
+ p_value = column_recovery(cpdb_mapping_result, 0)
+ m_inp_ol = column_recovery(cpdb_mapping_result, 8)
l_to_return = []
for num_path_t, l_p_m in enumerate(l_path_metabo):
path_cont = []
@@ -130,6 +135,8 @@ def recup_cpdb_pathways_list(cpdb_mapping_result, correspondence_file):
path_cont. append(str(l_p_m))
paths_to_rec = cor_index(path_cont, associated_chebi, associated_name)
paths_to_rec.insert(0, l_pathways[num_path_t])
+ paths_to_rec.insert(0, m_inp_ol[num_path_t + 1])
+ paths_to_rec.insert(0, p_value[num_path_t + 1])
l_to_return.append(paths_to_rec)
return l_to_return
@@ -398,25 +405,14 @@ def c_p_o_m_r(file, outf, mapper, type_of_view="all", save_plot="all",
else:
n_c = int(input('how many columns are there in the file?'))
l_of_pathways_list = recup_ma_pathways_list(file, n_c)
-
-
-
-
-
-
-
-
-
-
-
-
- if modul != None:
+ if modul == True:
list_path = []
up = []
down = []
log_p = []
metabo = column_recovery(f_modul, 0)
value_modul = column_recovery(f_modul, 1)
+ #print(l_of_pathways_list)
for i_p_l, path_l in enumerate(l_of_pathways_list):
l_of_pathways_list[i_p_l][2] = comma_cleaning(path_l[2])
if modul == True:
@@ -425,15 +421,43 @@ def c_p_o_m_r(file, outf, mapper, type_of_view="all", save_plot="all",
list_path.append(l_of_pathways_list[i_p_l][2])
for path_meta in path_l[3:]:
# print(comma_cleaning(path_meta)) Probable probléme de version entre ME et les autres (a vériifer)
- if float(value_modul[metabo.index(comma_cleaning(path_meta))]) >= 0:
- actu_up += 1
+ #print(path_meta)
+ if mapper == "ME":
+ if float(value_modul[metabo.index(comma_cleaning(path_meta))]) >= 0:
+ actu_up += 1
+ else:
+ actu_down += 1
else:
- actu_down += 1
- up.append((actu_up/path_l[1])*100)
- down.append((actu_down/path_l[1])*100)
- log_p.append(-log(path_l[0]))
+ if float(value_modul[metabo.index(path_meta)]) >= 0:
+ actu_up += 1
+ else:
+ actu_down += 1
+ up.append((actu_up/int(path_l[1]))*100)
+ down.append((actu_down/int(path_l[1]))*100)
+ log_p.append(-log(float(path_l[0])))
if modul == True:
- up_down_path_plot(list_path, up, down, log_p)
+ n_m_i_p = 200
+ if len(log_p) > n_m_i_p:
+ print(len(log_p))
+ under_plot = floor(len(log_p)/n_m_i_p)
+ print(floor(len(log_p)/n_m_i_p))
+ for plot in range(under_plot):
+ up_u_p = up[n_m_i_p*plot:n_m_i_p*plot+n_m_i_p]
+ down_u_p = down[n_m_i_p*plot:n_m_i_p*plot+n_m_i_p]
+ log_p_u_p = log_p[n_m_i_p*plot:n_m_i_p*plot+n_m_i_p]
+ list_path_u_p = list_path[n_m_i_p*plot:n_m_i_p*plot+n_m_i_p]
+ plot_u = up_down_path_plot(list_path_u_p, up_u_p, down_u_p, log_p_u_p)
+ plt.savefig(fold_of_visu_sav+"up_down_path_plot"+str(plot)+".png")
+ #plt.show()
+ up_u_p = up[n_m_i_p*plot+n_m_i_p:]
+ down_u_p = down[n_m_i_p*plot+n_m_i_p:]
+ log_p_u_p = log_p[n_m_i_p*plot+n_m_i_p:]
+ list_path_u_p = list_path[n_m_i_p*plot+n_m_i_p:]
+ plot_u = up_down_path_plot(list_path_u_p, up_u_p, down_u_p, log_p_u_p)
+ plt.savefig(fold_of_visu_sav+"up_down_path_plot"+str(under_plot + 1)+".png")
+ else :
+ plot = up_down_path_plot(list_path, up, down, log_p)
+ plt.savefig(fold_of_visu_sav+"up_down_path_plot.png")
if midfile == "Yes":
mid_data = pd.DataFrame(l_of_pathways_list, dtype=object)
excel_file_writer(mid_data, midfile_name, sheetname="Resultats")
@@ -591,10 +615,15 @@ def c_p_o_m_r(file, outf, mapper, type_of_view="all", save_plot="all",
if __name__ == "__main__":
+ #MAP = 'RAMP'
+ #MAP = "CPDB"
MAP = "ME"
VIEW = "all"
SAVE = "no"
+ #INFILE = LOCAL + "CPDB\\Resultats_mapping_Chebi_ID_L100_CPDB.csv"
INFILE = "ExportExcel_6843"
+ #INFILE = LOCAL + "RAMP\\sortie_Mapping_RAMP_L100_CheEBI.csv"
FINISHFILE = LOCAL + "test.xlsx"
FILE_MODUL = LOCAL + "L100_modulation_artificielle_HumanCyc.csv"
+ #FILE_MODUL = LOCAL + "CPDB\\liste_Chebi_des_100_chebi_ConsensusPAthDB_modul.csv"
c_p_o_m_r(INFILE, FINISHFILE, MAP, type_of_view=VIEW, save_plot=SAVE, modul=True, f_modul=FILE_MODUL)
--
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