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Commit 8bf3898b authored by Schneider Leo's avatar Schneider Leo
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datasets

parent 939cddd6
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...@@ -3,6 +3,7 @@ import numpy as np ...@@ -3,6 +3,7 @@ import numpy as np
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import pandas as pd import pandas as pd
import scipy.signal import scipy.signal
from PIL.ImageOps import cover
def compute_chromatograms(rt, mz, intensity, start_c, end_c): def compute_chromatograms(rt, mz, intensity, start_c, end_c):
...@@ -99,6 +100,10 @@ def integrated_mz_int(mz_list,int_list,mz_bin, mz_ref): ...@@ -99,6 +100,10 @@ def integrated_mz_int(mz_list,int_list,mz_bin, mz_ref):
res[int((mz_list[i] - min_mz) // mz_bin)] += int_list[i] res[int((mz_list[i] - min_mz) // mz_bin)] += int_list[i]
return res return res
def intensity_coverage(int_expe,int_theo):
coverage = np.sum(np.where(int_theo>0,int_expe,0))/np.sum(int_expe)
return coverage
if __name__ == "__main__": if __name__ == "__main__":
e = oms.MSExperiment() e = oms.MSExperiment()
oms.MzMLFile().load("data/echantillons données DIA/CITAMA-5-AER-d200.mzML", e) oms.MzMLFile().load("data/echantillons données DIA/CITAMA-5-AER-d200.mzML", e)
...@@ -158,10 +163,12 @@ if __name__ == "__main__": ...@@ -158,10 +163,12 @@ if __name__ == "__main__":
plt.savefig('fig/local_inte_res/spec_large_theo_1.png') plt.savefig('fig/local_inte_res/spec_large_theo_1.png')
plt.clf() plt.clf()
int_theo_inte_peak = integrated_mz_int(masses_1, intensities_1, 0.25, mz1) int_theo_inte_peak_1 = integrated_mz_int(masses_1, intensities_1, 0.25, mz1)
int_theo_inte_large = integrated_mz_int(masses_1, intensities_1, 0.25, mz1_large) int_theo_inte_large_1 = integrated_mz_int(masses_1, intensities_1, 0.25, mz1_large)
res_peak_1 = scipy.stats.pearsonr(int_theo_inte_peak, inty1) res_peak_1 = scipy.stats.pearsonr(int_theo_inte_peak_1, inty1)
res_large_1 = scipy.stats.pearsonr(int_theo_inte_large, inty1_large) coverage_peak_1 = intensity_coverage(inty1,int_theo_inte_peak_1)
res_large_1 = scipy.stats.pearsonr(int_theo_inte_large_1, inty1_large)
coverage_large_1 = intensity_coverage(inty1_large, int_theo_inte_large_1)
df_large_2 = df[df['MSlevel'] == 2] df_large_2 = df[df['MSlevel'] == 2]
df_large_2 = df_large_2[619 < df_large_2['MS1_mz_max']] df_large_2 = df_large_2[619 < df_large_2['MS1_mz_max']]
...@@ -201,5 +208,11 @@ if __name__ == "__main__": ...@@ -201,5 +208,11 @@ if __name__ == "__main__":
plt.savefig('fig/local_inte_res/spec_large_theo_2.png') plt.savefig('fig/local_inte_res/spec_large_theo_2.png')
plt.clf() plt.clf()
int_theo_inte_peak_2 = integrated_mz_int(masses_2, intensities_2, 0.25, mz2)
int_theo_inte_large_2 = integrated_mz_int(masses_2, intensities_2, 0.25, mz2_large)
res_peak_2 = scipy.stats.pearsonr(int_theo_inte_peak_2, inty2)
coverage_peak_2 = intensity_coverage(inty2,int_theo_inte_peak_2)
res_large_2 = scipy.stats.pearsonr(int_theo_inte_large_2, inty2_large)
coverage_large_2 = intensity_coverage(inty2_large, int_theo_inte_large_2)
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