From 6230382b79d34ffe8fc51c923b5f0a3ca0529b1c Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Tue, 1 Oct 2024 16:46:56 +0200
Subject: [PATCH] local integration working
---
local_integration_msms.py | 63 +++++++++++++++++++++++++++++++--------
1 file changed, 51 insertions(+), 12 deletions(-)
diff --git a/local_integration_msms.py b/local_integration_msms.py
index 2e5723f..17c67ab 100644
--- a/local_integration_msms.py
+++ b/local_integration_msms.py
@@ -27,23 +27,28 @@ def get_df(expe, long: bool = False):
"""
- cols = ["RT", "mzarray", "intarray", 'MSlevel','MS1 MZ']
+ cols = ["RT", "mzarray", "intarray", 'MSlevel','MS1_mz_min','MS1_mz_max']
- df = pd.DataFrame(data=((spec.getRT(), *spec.get_peaks(), spec.getMSLevel(), spec.getPrecursors()[0].getMZ() if spec.getMSLevel() ==2 else None) for spec in expe), columns=cols)
+ df = pd.DataFrame(data=((spec.getRT(), *spec.get_peaks(), spec.getMSLevel(),
+ spec.getPrecursors()[0].getMZ() - spec.getPrecursors()[0].getIsolationWindowLowerOffset() if spec.getMSLevel()==2 else None,
+ spec.getPrecursors()[0].getMZ() + spec.getPrecursors()[0].getIsolationWindowUpperOffset() if spec.getMSLevel()==2 else None
+ ) for spec in expe), columns=cols)
if long:
RT = []
mz = []
inty = []
ms_lv = []
- ms1_mz = []
+ ms1_mz_min = []
+ ms1_mz_max = []
for index, row in df.iterrows():
mz.extend(row['mzarray'])
inty.extend(row['intarray'])
RT.extend([row['RT']]*len(row['intarray']))
ms_lv.extend([row['MSlevel']] * len(row['intarray']))
- ms1_mz.extend([row['MS1 MZ']] * len(row['intarray']))
- dico = {"RT": RT, "mz": mz, "inty": inty, "MSlevel": ms_lv, "MS1 MZ": ms1_mz}
+ ms1_mz_min.extend([row['MS1_mz_min']] * len(row['intarray']))
+ ms1_mz_max.extend([row['MS1_mz_max']] * len(row['intarray']))
+ dico = {"RT": RT, "mz": mz, "inty": inty, "MSlevel": ms_lv, "MS1_mz_min": ms1_mz_min, "MS1_mz_max": ms1_mz_max}
return pd.DataFrame(dico)
else :
@@ -71,13 +76,21 @@ def generate_RT_int_imgs(exp,star_mz,stop_mz):
plt.savefig('fig/rt_local/{}_to_{}.png'.format(mz_range[i] ,mz_range[i+1]))
plt.clf()
-def integrate_ms_ms(time_start, time_end, df):
- df_useful = df[(df['MS1 RT']>time_start) & (df['MS1 RT']<time_end) & (df['MSlevel']==2)].reset_index(inplace=True)
-
- value = 0
-
-
- return value
+def integrate_ms_ms(df, mz_bin, output='temp.png', display = False):
+ # df_useful = df[(df['MS1 RT']>time_start) & (df['MS1 RT']<time_end) & (df['MSlevel']==2)].reset_index(inplace=True)
+ min_mz, max_mz = min(df['mz']), max(df['mz'])
+ mz_list = np.linspace(min_mz,max_mz,num = int((max_mz-min_mz)//mz_bin)+1)
+ int_list = np.zeros(int((max_mz-min_mz)//mz_bin)+1)
+ for index, row in df.iterrows():
+ int_list[int((row['mz']-min_mz)//mz_bin)]+=row['inty']
+ if display :
+ plt.clf()
+ fig, ax = plt.subplots()
+ ax.plot(mz_list, int_list,linewidth=0.1)
+ ax.set_xlim(200,1800)
+ plt.savefig(output)
+ plt.clf()
+ return mz_list,int_list
if __name__ == "__main__":
e = oms.MSExperiment()
@@ -97,4 +110,30 @@ if __name__ == "__main__":
ax.plot(mz_sorted,inty_sorted)
plt.savefig('temp.png')
+
+ #pic d'étude 462-468
+ #mz 750.13
+ df_peak = df[df['MSlevel'] == 2]
+ df_peak = df_peak[750.1 < df_peak['MS1_mz_max']]
+ df_peak = df_peak[750.1 > df_peak['MS1_mz_min']]
+ df_peak = df_peak[465 < df_peak['RT']]
+ df_peak = df_peak[466 > df_peak['RT']]
+
+
+ df_peak2 = df[df['MSlevel'] == 2]
+ df_peak2 = df_peak2[750.1 < df_peak2['MS1_mz_max']]
+ df_peak2 = df_peak2[750.1 > df_peak2['MS1_mz_min']]
+ df_peak2 = df_peak2[463 < df_peak2['RT']]
+ df_peak2 = df_peak2[467 > df_peak2['RT']]
+
+ mz1, inty1 = integrate_ms_ms(df_peak, 1)
+ mz2, inty2 = integrate_ms_ms(df_peak2, 1)
+ plt.clf()
+ fig, ax = plt.subplots()
+ ax.plot(mz1, inty1, linewidth=0.3)
+ ax.plot(mz2, inty2, linewidth=0.3)
+ ax.set_xlim(200, 1800)
+ plt.savefig('spec_combined.png')
+ plt.clf()
+
#358.1 358.32
\ No newline at end of file
--
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