571 lines
18 KiB
Python
571 lines
18 KiB
Python
# %% Scatter
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import pandas as pd
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import matplotlib.pyplot as plt
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import numpy as np
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# Load your data from TSV file
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/join_MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_results+MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Replace comma with dot for numeric conversion in GT_EDSS and LLM_Results
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df['GT_EDSS'] = df['GT_EDSS'].astype(str).str.replace(',', '.')
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df['LLM_Results'] = df['LLM_Results'].astype(str).str.replace(',', '.')
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# Convert to float (handle invalid entries gracefully)
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df['GT_EDSS'] = pd.to_numeric(df['GT_EDSS'], errors='coerce')
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df['LLM_Results'] = pd.to_numeric(df['LLM_Results'], errors='coerce')
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# Drop rows where either column is NaN
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df_clean = df.dropna(subset=['GT_EDSS', 'LLM_Results'])
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# Create scatter plot
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plt.figure(figsize=(8, 6))
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plt.scatter(df_clean['GT_EDSS'], df_clean['LLM_Results'], alpha=0.7, color='blue')
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# Add labels and title
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plt.xlabel('GT_EDSS')
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plt.ylabel('LLM_Results')
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plt.title('Comparison of GT_EDSS vs LLM_Results')
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# Optional: Add a diagonal line for reference (perfect prediction)
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plt.plot([0, max(df_clean['GT_EDSS'])], [0, max(df_clean['GT_EDSS'])], color='red', linestyle='--', label='Perfect Prediction')
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plt.legend()
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# Show plot
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plt.grid(True)
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plt.tight_layout()
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plt.show()
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##
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# %% Bland0-altman
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import pandas as pd
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import matplotlib.pyplot as plt
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import numpy as np
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import statsmodels.api as sm
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# Load your data from TSV file
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/join_MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_results+MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Replace comma with dot for numeric conversion in GT_EDSS and LLM_Results
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df['GT_EDSS'] = df['GT_EDSS'].astype(str).str.replace(',', '.')
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df['LLM_Results'] = df['LLM_Results'].astype(str).str.replace(',', '.')
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# Convert to float (handle invalid entries gracefully)
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df['GT_EDSS'] = pd.to_numeric(df['GT_EDSS'], errors='coerce')
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df['LLM_Results'] = pd.to_numeric(df['LLM_Results'], errors='coerce')
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# Drop rows where either column is NaN
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df_clean = df.dropna(subset=['GT_EDSS', 'LLM_Results'])
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# Create Bland-Altman plot
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f, ax = plt.subplots(1, figsize=(8, 5))
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sm.graphics.mean_diff_plot(df_clean['GT_EDSS'], df_clean['LLM_Results'], ax=ax)
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# Add labels and title
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ax.set_title('Bland-Altman Plot: GT_EDSS vs LLM_Results')
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ax.set_xlabel('Mean of GT_EDSS and LLM_Results')
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ax.set_ylabel('Difference between GT_EDSS and LLM_Results')
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# Display Bland-Altman plot
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plt.tight_layout()
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plt.show()
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# Print some statistics
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mean_diff = np.mean(df_clean['GT_EDSS'] - df_clean['LLM_Results'])
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std_diff = np.std(df_clean['GT_EDSS'] - df_clean['LLM_Results'])
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print(f"Mean difference: {mean_diff:.3f}")
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print(f"Standard deviation of differences: {std_diff:.3f}")
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print(f"95% Limits of Agreement: [{mean_diff - 1.96*std_diff:.3f}, {mean_diff + 1.96*std_diff:.3f}]")
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##
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# %% Confusion matrix
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import pandas as pd
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import matplotlib.pyplot as plt
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import numpy as np
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from sklearn.metrics import confusion_matrix, classification_report
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import seaborn as sns
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# Load your data from TSV file
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/join_results_unique.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Replace comma with dot for numeric conversion in GT_EDSS and LLM_Results
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df['GT_EDSS'] = df['GT_EDSS'].astype(str).str.replace(',', '.')
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df['LLM_Results'] = df['LLM_Results'].astype(str).str.replace(',', '.')
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# Convert to float (handle invalid entries gracefully)
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df['GT_EDSS'] = pd.to_numeric(df['GT_EDSS'], errors='coerce')
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df['LLM_Results'] = pd.to_numeric(df['LLM_Results'], errors='coerce')
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# Drop rows where either column is NaN
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df_clean = df.dropna(subset=['GT_EDSS', 'LLM_Results'])
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# For confusion matrix, we need to categorize the values
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# Let's create categories up to 10 (0-1, 1-2, 2-3, ..., 9-10)
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def categorize_edss(value):
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if pd.isna(value):
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return np.nan
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elif value <= 1.0:
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return '0-1'
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elif value <= 2.0:
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return '1-2'
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elif value <= 3.0:
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return '2-3'
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elif value <= 4.0:
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return '3-4'
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elif value <= 5.0:
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return '4-5'
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elif value <= 6.0:
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return '5-6'
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elif value <= 7.0:
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return '6-7'
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elif value <= 8.0:
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return '7-8'
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elif value <= 9.0:
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return '8-9'
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elif value <= 10.0:
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return '9-10'
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else:
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return '10+'
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# Create categorical versions
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df_clean['GT_EDSS_cat'] = df_clean['GT_EDSS'].apply(categorize_edss)
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df_clean['LLM_Results_cat'] = df_clean['LLM_Results'].apply(categorize_edss)
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# Remove any NaN categories
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df_clean = df_clean.dropna(subset=['GT_EDSS_cat', 'LLM_Results_cat'])
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# Create confusion matrix
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cm = confusion_matrix(df_clean['GT_EDSS_cat'], df_clean['LLM_Results_cat'],
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labels=['0-1', '1-2', '2-3', '3-4', '4-5', '5-6', '6-7', '7-8', '8-9', '9-10'])
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# Plot confusion matrix
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plt.figure(figsize=(10, 8))
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sns.heatmap(cm, annot=True, fmt='d', cmap='Blues',
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xticklabels=['0-1', '1-2', '2-3', '3-4', '4-5', '5-6', '6-7', '7-8', '8-9', '9-10'],
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yticklabels=['0-1', '1-2', '2-3', '3-4', '4-5', '5-6', '6-7', '7-8', '8-9', '9-10'])
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plt.title('Confusion Matrix: GT_EDSS vs interferred EDSS (Categorized 0-10)')
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plt.xlabel('LLM_Results Category')
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plt.ylabel('GT_EDSS Category')
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plt.tight_layout()
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plt.show()
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# Print classification report
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print("Classification Report:")
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print(classification_report(df_clean['GT_EDSS_cat'], df_clean['LLM_Results_cat']))
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# Print raw counts
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print("\nConfusion Matrix (Raw Counts):")
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print(cm)
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##
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# %% Classification
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import pandas as pd
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import matplotlib.pyplot as plt
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import seaborn as sns
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from sklearn.metrics import confusion_matrix
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import numpy as np
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# Load your data from TSV file
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file_path ='/home/shahin/Lab/Doktorarbeit/Barcelona/Data/join_results_unique.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Check data structure
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print("Data shape:", df.shape)
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print("First few rows:")
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print(df.head())
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print("\nColumn names:")
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for col in df.columns:
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print(f" {col}")
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# Function to safely convert to boolean
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def safe_bool_convert(series):
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'''Safely convert series to boolean, handling various input formats'''
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# Convert to string first, then to boolean
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series_str = series.astype(str).str.strip().str.lower()
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# Handle different true/false representations
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bool_map = {
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'true': True, '1': True, 'yes': True, 'y': True,
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'false': False, '0': False, 'no': False, 'n': False
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}
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converted = series_str.map(bool_map)
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# Handle remaining NaN values
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converted = converted.fillna(False) # or True, depending on your preference
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return converted
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# Convert columns safely
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if 'LLM_klassifizierbar' in df.columns:
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print("\nLLM_klassifizierbar column info:")
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print(df['LLM_klassifizierbar'].head(10))
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print("Unique values:", df['LLM_klassifizierbar'].unique())
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df['LLM_klassifizierbar'] = safe_bool_convert(df['LLM_klassifizierbar'])
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print("After conversion:")
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print(df['LLM_klassifizierbar'].value_counts())
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if 'GT_klassifizierbar' in df.columns:
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print("\nGT_klassifizierbar column info:")
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print(df['GT_klassifizierbar'].head(10))
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print("Unique values:", df['GT_klassifizierbar'].unique())
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df['GT_klassifizierbar'] = safe_bool_convert(df['GT_klassifizierbar'])
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print("After conversion:")
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print(df['GT_klassifizierbar'].value_counts())
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# Create bar chart showing only True values for klassifizierbar
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if 'LLM_klassifizierbar' in df.columns and 'GT_klassifizierbar' in df.columns:
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# Get counts for True values only
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llm_true_count = df['LLM_klassifizierbar'].sum()
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gt_true_count = df['GT_klassifizierbar'].sum()
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# Plot using matplotlib directly
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fig, ax = plt.subplots(figsize=(8, 6))
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x = np.arange(2)
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width = 0.35
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bars1 = ax.bar(x[0] - width/2, llm_true_count, width, label='LLM', color='skyblue', alpha=0.8)
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bars2 = ax.bar(x[1] + width/2, gt_true_count, width, label='GT', color='lightcoral', alpha=0.8)
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# Add value labels on bars
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ax.annotate(f'{llm_true_count}',
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xy=(x[0], llm_true_count),
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xytext=(0, 3),
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textcoords="offset points",
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ha='center', va='bottom')
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ax.annotate(f'{gt_true_count}',
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xy=(x[1], gt_true_count),
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xytext=(0, 3),
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textcoords="offset points",
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ha='center', va='bottom')
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ax.set_xlabel('Classification Status (klassifizierbar)')
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ax.set_ylabel('Count')
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ax.set_title('True Values Comparison: LLM vs GT for "klassifizierbar"')
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ax.set_xticks(x)
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ax.set_xticklabels(['LLM', 'GT'])
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ax.legend()
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plt.tight_layout()
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plt.show()
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# Create confusion matrix if both columns exist
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if 'LLM_klassifizierbar' in df.columns and 'GT_klassifizierbar' in df.columns:
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try:
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# Ensure both columns are boolean
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llm_bool = df['LLM_klassifizierbar'].fillna(False).astype(bool)
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gt_bool = df['GT_klassifizierbar'].fillna(False).astype(bool)
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cm = confusion_matrix(gt_bool, llm_bool)
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# Plot confusion matrix
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fig, ax = plt.subplots(figsize=(8, 6))
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sns.heatmap(cm, annot=True, fmt='d', cmap='Blues',
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xticklabels=['False ', 'True '],
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yticklabels=['False', 'True '],
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ax=ax)
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ax.set_xlabel('LLM Predictions ')
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ax.set_ylabel('GT Labels ')
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ax.set_title('Confusion Matrix: LLM vs GT for "klassifizierbar"')
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plt.tight_layout()
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plt.show()
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print("Confusion Matrix:")
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print(cm)
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except Exception as e:
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print(f"Error creating confusion matrix: {e}")
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# Show final data info
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print("\nFinal DataFrame info:")
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print(df[['LLM_klassifizierbar', 'GT_klassifizierbar']].info())
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##
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# %% Boxplot
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import pandas as pd
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import matplotlib.pyplot as plt
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import seaborn as sns
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import numpy as np
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# Load your data from TSV file
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/join_results_unique.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Replace comma with dot for numeric conversion in GT_EDSS and LLM_Results
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df['GT_EDSS'] = df['GT_EDSS'].astype(str).str.replace(',', '.')
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df['LLM_Results'] = df['LLM_Results'].astype(str).str.replace(',', '.')
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# Convert to float (handle invalid entries gracefully)
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df['GT_EDSS'] = pd.to_numeric(df['GT_EDSS'], errors='coerce')
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df['LLM_Results'] = pd.to_numeric(df['LLM_Results'], errors='coerce')
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# Drop rows where either column is NaN
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df_clean = df.dropna(subset=['GT_EDSS', 'LLM_Results'])
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# 1. DEFINE CATEGORY ORDER
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# This ensures the X-axis is numerically logical (0-1 comes before 1-2)
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category_order = ['0-1', '1-2', '2-3', '3-4', '4-5', '5-6', '6-7', '7-8', '8-9', '9-10', '10+']
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# Convert the column to a Categorical type with the specific order
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df_clean['GT_EDSS_cat'] = pd.Categorical(df_clean['GT_EDSS'].apply(categorize_edss),
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categories=category_order,
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ordered=True)
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plt.figure(figsize=(14, 8))
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# 2. ADD HUE FOR LEGEND
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# Assigning x to 'hue' allows Seaborn to generate a legend automatically
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box_plot = sns.boxplot(
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data=df_clean,
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x='GT_EDSS_cat',
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y='LLM_Results',
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hue='GT_EDSS_cat', # Added hue
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palette='viridis',
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linewidth=1.5,
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legend=True # Ensure legend is enabled
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)
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# 3. CUSTOMIZE PLOT
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plt.title('Distribution of LLM_Results by GT_EDSS Category', fontsize=18, pad=20)
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plt.xlabel('Ground Truth EDSS Category', fontsize=14)
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plt.ylabel('LLM Predicted EDSS', fontsize=14)
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# Move legend to the side or top
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plt.legend(title="EDSS Categories", bbox_to_anchor=(1.05, 1), loc='upper left')
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plt.xticks(rotation=45, ha='right', fontsize=10)
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plt.grid(True, axis='y', alpha=0.3)
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plt.tight_layout()
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plt.show()
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##
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# %% Postproccessing Column names
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import pandas as pd
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# Read the TSV file
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/Join_edssandsub.tsv'
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df = pd.read_csv(file_path, sep='\t')
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# Create a mapping dictionary for German to English column names
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column_mapping = {
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'EDSS':'GT.EDSS',
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'klassifizierbar': 'GT.klassifizierbar',
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'Sehvermögen': 'GT.VISUAL_OPTIC_FUNCTIONS',
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'Cerebellum': 'GT.CEREBELLAR_FUNCTIONS',
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'Hirnstamm': 'GT.BRAINSTEM_FUNCTIONS',
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'Sensibiliät': 'GT.SENSORY_FUNCTIONS',
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'Pyramidalmotorik': 'GT.PYRAMIDAL_FUNCTIONS',
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'Ambulation': 'GT.AMBULATION',
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'Cerebrale_Funktion': 'GT.CEREBRAL_FUNCTIONS',
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'Blasen-_und_Mastdarmfunktion': 'GT.BOWEL_AND_BLADDER_FUNCTIONS'
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}
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# Rename columns
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df = df.rename(columns=column_mapping)
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# Save the modified dataframe back to TSV file
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df.to_csv(file_path, sep='\t', index=False)
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print("Columns have been successfully renamed!")
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print("Renamed columns:")
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for old_name, new_name in column_mapping.items():
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if old_name in df.columns:
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print(f" {old_name} -> {new_name}")
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##
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# %% Styled table
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import pandas as pd
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import numpy as np
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import seaborn as sns
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import matplotlib.pyplot as plt
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import dataframe_image as dfi
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# Load data
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df = pd.read_csv("/home/shahin/Lab/Doktorarbeit/Barcelona/Data/Join_edssandsub.tsv", sep='\t')
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# 1. Identify all GT and result columns
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gt_columns = [col for col in df.columns if col.startswith('GT.')]
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result_columns = [col for col in df.columns if col.startswith('result.')]
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print("GT Columns found:", gt_columns)
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print("Result Columns found:", result_columns)
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# 2. Create proper mapping between GT and result columns
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# Handle various naming conventions (spaces, underscores, etc.)
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column_mapping = {}
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for gt_col in gt_columns:
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base_name = gt_col.replace('GT.', '')
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# Clean the base name for matching - remove spaces, underscores, etc.
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# Try different matching approaches
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candidates = [
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f'result.{base_name}', # Exact match
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f'result.{base_name.replace(" ", "_")}', # With underscores
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f'result.{base_name.replace("_", " ")}', # With spaces
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f'result.{base_name.replace(" ", "")}', # No spaces
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f'result.{base_name.replace("_", "")}' # No underscores
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]
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# Also try case-insensitive matching
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candidates.append(f'result.{base_name.lower()}')
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candidates.append(f'result.{base_name.upper()}')
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# Try to find matching result column
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matched = False
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for candidate in candidates:
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if candidate in result_columns:
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column_mapping[gt_col] = candidate
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matched = True
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break
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# If no exact match found, try partial matching
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if not matched:
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# Try to match by removing special characters and comparing
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base_clean = ''.join(e for e in base_name if e.isalnum() or e in ['_', ' '])
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for result_col in result_columns:
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result_base = result_col.replace('result.', '')
|
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result_clean = ''.join(e for e in result_base if e.isalnum() or e in ['_', ' '])
|
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if base_clean.lower() == result_clean.lower():
|
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column_mapping[gt_col] = result_col
|
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matched = True
|
|
break
|
|
|
|
print("Column mapping:", column_mapping)
|
|
|
|
# 3. Faster, vectorized computation using the corrected mapping
|
|
data_list = []
|
|
|
|
for gt_col, result_col in column_mapping.items():
|
|
print(f"Processing {gt_col} vs {result_col}")
|
|
|
|
# Convert to numeric, forcing errors to NaN
|
|
s1 = pd.to_numeric(df[gt_col], errors='coerce').astype(float)
|
|
s2 = pd.to_numeric(df[result_col], errors='coerce').astype(float)
|
|
|
|
# Calculate matches (abs difference <= 0.5)
|
|
diff = np.abs(s1 - s2)
|
|
matches = (diff <= 0.5).sum()
|
|
|
|
# Determine the denominator (total valid comparisons)
|
|
valid_count = diff.notna().sum()
|
|
|
|
if valid_count > 0:
|
|
percentage = (matches / valid_count) * 100
|
|
else:
|
|
percentage = 0
|
|
|
|
# Extract clean base name for display
|
|
base_name = gt_col.replace('GT.', '')
|
|
|
|
data_list.append({
|
|
'GT': base_name,
|
|
'Match %': round(percentage, 1)
|
|
})
|
|
|
|
|
|
|
|
|
|
# 4. Prepare Data
|
|
match_df = pd.DataFrame(data_list)
|
|
# Clean up labels: Replace underscores with spaces and capitalize
|
|
match_df['GT'] = match_df['GT'].str.replace('_', ' ').str.title()
|
|
match_df = match_df.sort_values('Match %', ascending=False)
|
|
|
|
# 5. Create a "Beautiful" Table using Seaborn Heatmap
|
|
def create_luxury_table(df, output_file="edss_agreement.png"):
|
|
# Set the aesthetic style
|
|
sns.set_theme(style="white", font="sans-serif")
|
|
|
|
# Prepare data for heatmap
|
|
plot_data = df.set_index('GT')[['Match %']]
|
|
|
|
# Initialize the figure
|
|
# Height is dynamic based on number of rows
|
|
fig, ax = plt.subplots(figsize=(8, len(df) * 0.6))
|
|
|
|
# Create a custom diverging color map (Deep Red -> Mustard -> Emerald)
|
|
# This looks more professional than standard 'RdYlGn'
|
|
cmap = sns.diverging_palette(15, 135, s=80, l=55, as_cmap=True)
|
|
|
|
# Draw the heatmap
|
|
sns.heatmap(
|
|
plot_data,
|
|
annot=True,
|
|
fmt=".1f",
|
|
cmap=cmap,
|
|
center=85, # Centers the color transition
|
|
vmin=50, vmax=100, # Range of the gradient
|
|
linewidths=2,
|
|
linecolor='white',
|
|
cbar=False, # Remove color bar for a "table" look
|
|
annot_kws={"size": 14, "weight": "bold", "family": "sans-serif"}
|
|
)
|
|
|
|
# Styling the Axes (Turning the heatmap into a table)
|
|
ax.set_xlabel("")
|
|
ax.set_ylabel("")
|
|
ax.xaxis.tick_top() # Move "Match %" label to top
|
|
ax.set_xticklabels(['Agreement (%)'], fontsize=14, fontweight='bold', color='#2c3e50')
|
|
ax.tick_params(axis='y', labelsize=12, labelcolor='#2c3e50', length=0)
|
|
|
|
# Add a thin border around the plot
|
|
for _, spine in ax.spines.items():
|
|
spine.set_visible(True)
|
|
spine.set_color('#ecf0f1')
|
|
|
|
plt.title('EDSS Subcategory Consistency Analysis', fontsize=16, pad=40, fontweight='bold', color='#2c3e50')
|
|
|
|
# Add a subtle footer
|
|
plt.figtext(0.5, 0.02, "Tolerance: ±0.5 points | N = [Total Samples]",
|
|
wrap=True, horizontalalignment='center', fontsize=10, color='gray', style='italic')
|
|
|
|
# Save with high resolution
|
|
plt.tight_layout()
|
|
plt.savefig(output_file, dpi=300, bbox_inches='tight')
|
|
print(f"Beautiful table saved as {output_file}")
|
|
|
|
# Execute
|
|
create_luxury_table(match_df)
|
|
|
|
|
|
# Run the function
|
|
save_styled_table(match_df)
|
|
# 6. Save as SVG
|
|
|
|
#plt.savefig("agreement_table.svg", format='svg', dpi=300, bbox_inches='tight')
|
|
#print("Successfully saved agreement_table.svg")
|
|
|
|
# Show plot if running in a GUI environment
|
|
plt.show()
|
|
|
|
##
|