From 2d98534b78b350d71003197ff9f2d99be6255683 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Thu, 23 Jan 2025 15:23:40 +0100
Subject: [PATCH] data viz
---
data/data_processing.py | 1 -
data/data_viz.py | 68 ++++++++++++++++++++++++++++++++++-------
2 files changed, 57 insertions(+), 12 deletions(-)
diff --git a/data/data_processing.py b/data/data_processing.py
index 0898283..a1ac05b 100644
--- a/data/data_processing.py
+++ b/data/data_processing.py
@@ -155,7 +155,6 @@ if __name__ == '__main__':
df_base = pd.read_csv('./data_PXD006109/plasma_train/data_aligned_train_plasma.csv')
df_base = df_base[['sequence', 'irt_scaled','state']]
t = [0.05,0.1,0.2,0.3,0.4,0.5,0.7,1,10]
- #reste 07 1 et all
name = ['005','01','02','03','04','05','07','1','all']
df_0 = pd.read_csv('../output/out_plasma_aligned_train_0.csv')
df_1 = pd.read_csv('../output/out_plasma_aligned_train_1.csv')
diff --git a/data/data_viz.py b/data/data_viz.py
index 42a5f82..f3ccbe1 100644
--- a/data/data_viz.py
+++ b/data/data_viz.py
@@ -166,26 +166,51 @@ def plot_res():
def calc_and_plot_res():
all_data=[]
base = 'out_'
- for name in ['early_stop_plasma_plasma','plasma_aug_005_plasma','plasma_aug_01_plasma',
- 'plasma_aug_02_plasma','plasma_aug_03_plasma','plasma_aug_04_plasma',
- 'plasma_aug_05_plasma','plasma_aug_07_plasma','plasma_aug_1_plasma',
- 'plasma_aug_all_plasma','prosit_plasma']:
+ for name in ['early_stop_plasma_plasma','plasma_train_augmented_005_plasma_train','plasma_train_augmented_01_plasma_train',
+ 'plasma_train_augmented_02_plasma_train','plasma_train_augmented_03_plasma_train','plasma_train_augmented_04_plasma_train',
+ 'plasma_train_augmented_05_plasma_train','plasma_train_augmented_07_plasma_train','plasma_train_augmented_1_plasma_train',
+ 'plasma_train_augmented_all_plasma_train','prosit_plasma']:
print(name)
r2_list=[]
for index in range(9):
dataframe = pd.read_csv('../output/'+base+name+'_'+str(index)+'.csv')
r2_list.append(r2_score(dataframe['true rt'], dataframe['rt pred']))
all_data.append(r2_list)
- fig, axs = plt.subplots(figsize=(9, 4))
- axs.boxplot(all_data)
- axs.set_title('Box plot')
+ fig, axs = plt.subplots(2, 1, figsize=(9, 8))
+ axs[0].boxplot(all_data)
+
+ axs[0].set_title('Box plot')
# adding horizontal grid lines
- axs.yaxis.grid(True)
- axs.set_xticks([y + 1 for y in range(len(all_data))],
+ axs[0].yaxis.grid(True)
+ axs[1].set_xticks([y for y in range(len(all_data))],
labels=[ 'plasma', 'Augm 0.05', 'Augm 0.1', 'Augm 0.2', 'Augm 0.3', 'Augm 0.4', 'Augm 0.5', 'Augm 0.7',
- 'Augm 1', 'Augm all', 'Prosit', ])
- plt.savefig('../fig/model perf/summary_early_stop_plasma.png')
+ 'Augm 1', 'Augm all', 'Prosit', ], rotation=30)
+ ref_path, base_path = './data_PXD006109/plasma_train/data_aligned_train_plasma.csv', './data_PXD006109/plasma_train/plasma_train_data_augmented_'
+ name = ['005','01','02','03','04','05','07','1','all']
+ df = pd.read_csv(ref_path)
+ size = [df.shape[0]]
+ x = [i for i in range(len(name)+2)]
+ for i in range(len(name)):
+ path = base_path+name[i]+'.csv'
+ df = pd.read_csv(path)
+ s = df.shape[0]
+
+
+ size.append(s)
+ df = pd.read_csv('./data_prosit/data.csv')
+ size.append(df.shape[0])
+ size = np.array(size)/max(size)
+ for i in range(len(size)):
+ axs[1].text(i, size[i], '{:.3f}'.format(size[i]), style='italic')
+ axs[0].text(i+0.5, np.mean(all_data[i])-0.01, f': {np.mean(all_data[i]):.3f}')
+ axs[1].plot(x,size)
+
+
+
+ plt.savefig('../fig/model perf/summary_early_stop_plasma_train.png')
+
+
def error_by_methionine(dataframe):
def fonc(a):
@@ -216,6 +241,27 @@ def filter_outlier_rt(dataframe):
plt.savefig('../fig/data_exploration/outlier_selection.png')
return df_out
+def plot_augmented_dataset_size(ref_path,base_path):
+ t = [0.05,0.1,0.2,0.3,0.4,0.5,0.7,1,10]
+ name = ['005','01','02','03','04','05','07','1','all']
+ df = pd.read_csv(ref_path)
+ size = [df.shape[0]]
+ x = [i for i in range(len(name)+1)]
+ for i in range(len(name)):
+ path = base_path+name[i]+'.csv'
+ df = pd.read_csv(path)
+ size.append(df.shape[0])
+ size = np.array(size)/max(size)
+ fig, ax = plt.subplots()
+ ax.plot(x,size)
+ ax.set_xticks([y + 1 for y in range(len(name)+1)],
+ labels=['base', 'Augm 0.05', 'Augm 0.1', 'Augm 0.2', 'Augm 0.3', 'Augm 0.4', 'Augm 0.5',
+ 'Augm 0.7',
+ 'Augm 1', 'Augm all'], rotation=30)
+
+ plt.savefig('../fig/data_exploration/augmented_dataset_size.png')
+
+
if __name__ == '__main__' :
calc_and_plot_res()
# base = ['plasma_plasma','plasma_prosit']
--
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