383 lines
12 KiB
Python
383 lines
12 KiB
Python
# %% Explore
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import pandas as pd
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# Load the dataset
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file_path = '/home/shahin/Lab/Doktorarbeit/Barcelona/Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv'
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df = pd.read_csv(file_path, sep=';')
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# Show basic information about the dataset
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print("Dataset shape:", df.shape)
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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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# Count unique patients
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unique_patients = df['unique_id'].nunique()
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print(f"\nNumber of unique patients: {unique_patients}")
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# Count how many times each patient appears
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patient_counts = df['unique_id'].value_counts()
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# Calculate average appearances per patient
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average_appearances = patient_counts.mean()
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# Show some statistics
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print(f"\nAverage number of times each patient appeared: {average_appearances:.2f}")
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print(f"\nMinimum appearances for any patient: {patient_counts.min()}")
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print(f"Maximum appearances for any patient: {patient_counts.max()}")
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# Show the first few patient counts
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print("\nFirst 10 patients and their appearance counts:")
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print(patient_counts.head(10))
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# Show how many patients appear exactly once
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single_occurrence = (patient_counts == 1).sum()
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print(f"\nNumber of patients who appeared exactly once: {single_occurrence}")
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# Show how many patients appear more than once
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multiple_occurrence = (patient_counts > 1).sum()
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print(f"Number of patients who appeared more than once: {multiple_occurrence}")
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##
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# %% EDSS Dist
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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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# Assuming your data is loaded into a DataFrame called 'df'
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# If you need to load from file:
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df = pd.read_csv('/home/shahin/Lab/Doktorarbeit/Barcelona/Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv', sep=';')
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# Create EDSS categories function with better error handling
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def categorize_edss(edss_value):
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# Handle NaN and empty values
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if pd.isna(edss_value) or edss_value == '' or edss_value is None:
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return 'No EDSS'
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# Convert to string and replace comma with dot
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edss_str = str(edss_value).strip()
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# Handle special cases
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if edss_str.lower() in ['unverändert', 'unchanged', 'n/a', 'na', 'none', 'null', '']:
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return 'Invalid'
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try:
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# Replace comma with dot for decimal numbers
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edss_str = edss_str.replace(',', '.')
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# Try to convert to float
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edss_float = float(edss_str)
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# Categorize based on value
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if 0 <= edss_float <= 1:
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return '0-1'
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elif 1 < edss_float <= 2:
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return '1-2'
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elif 2 < edss_float <= 3:
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return '2-3'
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elif 3 < edss_float <= 4:
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return '3-4'
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elif 4 < edss_float <= 5:
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return '4-5'
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elif 5 < edss_float <= 6:
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return '5-6'
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elif 6 < edss_float <= 7:
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return '6-7'
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elif 7 < edss_float <= 8:
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return '7-8'
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elif 8 < edss_float <= 9:
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return '8-9'
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elif 9 < edss_float <= 10:
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return '9-10'
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else:
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return 'Invalid'
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except (ValueError, TypeError):
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return 'Invalid'
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# Apply categorization
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df['EDSS_Category'] = df['EDSS'].apply(categorize_edss)
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# Count patients in each category
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edss_counts = df['EDSS_Category'].value_counts().sort_index()
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# Print the counts for reference
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print("Patient counts by EDSS category:")
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print(edss_counts)
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# Create the bar chart
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plt.figure(figsize=(12, 6))
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bars = plt.bar(edss_counts.index, edss_counts.values, color='skyblue', edgecolor='navy', alpha=0.7)
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# Add value labels on top of bars
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for bar in bars:
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height = bar.get_height()
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plt.text(bar.get_x() + bar.get_width()/2., height,
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f'{int(height)}',
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ha='center', va='bottom')
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plt.xlabel('EDSS Score Categories')
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plt.ylabel('Number of Cases')
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plt.title('Distribution of Patients by EDSS Score Categories')
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plt.xticks(rotation=45)
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plt.grid(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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# %% Pie Chart
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import matplotlib.pyplot as plt
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import pandas as pd
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# Your data
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data = {
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'Visit': [9, 8, 7, 6, 5, 4, 3, 2, 1],
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'patient_count': [2, 3, 3, 6, 13, 17, 28, 24, 32]
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}
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df = pd.DataFrame(data)
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# Create pie chart
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plt.figure(figsize=(10, 8))
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# Define colors for better visualization
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colors = ['#ff9999', '#66b3ff', '#99ff99', '#ffcc99', '#ff99cc',
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'#c2c2f0', '#ffb3b3', '#99ffcc', '#ffccff']
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# Create pie chart with custom labels showing both count and percentage
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labels = [f'{visit} Visits \n{count} patients\n({count/128*100:.1f}%)'
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for visit, count in zip(df['Visit'], df['patient_count'])]
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wedges, texts, autotexts = plt.pie(df['patient_count'],
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labels=labels,
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colors=colors,
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autopct='%1.1f%%',
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startangle=90,
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explode=[0.05] * len(df)) # Slightly separate slices
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# Add title
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plt.title('Patient Visit Frequency Distribution\nTotal Patients: 128\nTotal Cases: 396', fontsize=16, pad=20)
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# Ensure pie chart is circular
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plt.axis('equal')
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# Adjust layout to prevent legend cutoff
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plt.tight_layout()
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# Save as SVG (this will create a high-quality vector graphic)
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plt.savefig('patient_visit_frequency.svg', format='svg', bbox_inches='tight', dpi=300)
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# Also save as PNG for reference
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plt.savefig('patient_visit_frequency.png', format='png', bbox_inches='tight', dpi=300)
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# Show the chart
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plt.show()
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# Print summary statistics
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print(f"Total patients: {sum(df['patient_count'])}")
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print("\nVisit frequency breakdown:")
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for visit, count in zip(df['Visit'], df['patient_count']):
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percentage = (count / 128) * 100
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print(f"{visit} Visits : {count} patients ({percentage:.1f}%)")
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print("\nFiles created:")
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print("- patient_visit_frequency.svg (SVG format)")
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print("- patient_visit_frequency.png (PNG format)")
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##
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# %% Slope Chart
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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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# 1. Data Prep (Cleaning and filtering for patients with >1 visit)
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df['EDSS'] = pd.to_numeric(df['EDSS'].astype(str).str.replace(',', '.'), errors='coerce')
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df = df.dropna(subset=['unique_id', 'EDSS', 'MedDatum']).sort_values(['unique_id', 'MedDatum'])
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# Extract first and last
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first_last = df.groupby('unique_id').apply(lambda x: x.iloc[[0, -1]] if len(x) > 1 else None).reset_index(drop=True)
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first_last['Visit_Type'] = first_last.groupby('unique_id').cumcount().map({0: 'First Visit', 1: 'Last Visit'})
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# 2. Set the style
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sns.set_style("white")
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plt.figure(figsize=(10, 8))
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# Define sophisticated colors
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color_worsened = "#E67E22" # Muted Orange
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color_improved = "#2ECC71" # Muted Green
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color_stable = "#BDC3C7" # Soft Grey
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avg_color = "#2C3E50" # Deep Navy
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# 3. Plotting individual lines
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for pid in first_last['unique_id'].unique():
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p_data = first_last[first_last['unique_id'] == pid]
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start, end = p_data.iloc[0]['EDSS'], p_data.iloc[1]['EDSS']
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# Logic for color and linewidth
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if end > start:
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color, alpha, lw = color_worsened, 0.3, 1.2
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elif end < start:
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color, alpha, lw = color_improved, 0.3, 1.2
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else:
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color, alpha, lw = color_stable, 0.15, 0.8
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plt.plot(p_data['Visit_Type'], p_data['EDSS'],
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color=color, alpha=alpha, linewidth=lw, marker='o', markersize=4, markerfacecolor='white')
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# 4. Add Background Distribution (Violin Plot)
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sns.violinplot(x='Visit_Type', y='EDSS', data=first_last,
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inner=None, color=".95", linewidth=0)
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# 5. Add the Population Mean (The "Hero" line)
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summary = first_last.groupby('Visit_Type')['EDSS'].mean().reindex(['First Visit', 'Last Visit'])
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plt.plot(summary.index, summary.values, color=avg_color, linewidth=4,
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marker='s', markersize=10, label='Average Population Trend', zorder=10)
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# 6. Annotate the Average values
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for i, val in enumerate(summary.values):
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plt.text(i, val + 0.2, f'{val:.2f}', color=avg_color, fontweight='bold', ha='center')
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# Aesthetics
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plt.title('Evolution of EDSS Scores: First vs. Last Clinical Visit', fontsize=16, pad=20, fontweight='bold')
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plt.ylabel('EDSS Score', fontsize=12)
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plt.xlabel('')
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plt.xticks(fontsize=12, fontweight='bold')
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plt.yticks(np.arange(0, 10.5, 1)) # Typical EDSS scale
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plt.ylim(-0.5, 10)
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# Remove chart junk
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sns.despine(left=True, bottom=True)
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plt.grid(axis='y', color='gray', linestyle='--', alpha=0.2)
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plt.legend(frameon=False, loc='upper center', bbox_to_anchor=(0.5, -0.05))
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plt.tight_layout()
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plt.show()
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##
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# %% name
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import matplotlib.pyplot as plt
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# Data
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data = {
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'Visit': [9, 8, 7, 6, 5, 4, 3, 2, 1],
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'patient_count': [2, 3, 3, 6, 13, 17, 28, 24, 32]
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}
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# Create figure and axis
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fig, ax = plt.subplots(figsize=(10, 6))
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# Plot the bar chart
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bars = ax.bar(data['Visit'], data['patient_count'], color='darkblue', label='Patients by Visit Count')
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# Add labels and title
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ax.set_xlabel('Visit Number (from last to first)', fontsize=12)
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ax.set_ylabel('Number of Patients', fontsize=12)
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ax.set_title('Patient Visits by Visit Number', fontsize=14)
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# Invert x-axis to show Visit 9 on the left (descending order) if desired, but keep natural order (1–9 left to right)
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# For descending order (9→1 from left to right), we'd need to reverse:
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# Visit = data['Visit'][::-1], patient_count = data['patient_count'][::-1]
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# But standard practice is ascending (1 to 9), so we'll sort accordingly:
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# Let's sort by Visit to ensure left-to-right: 1,2,...,9
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# Actually, your current Visit list is [9,8,...,1], which is descending.
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# Let's sort by Visit for intuitive left-to-right increasing order:
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sorted_indices = sorted(range(len(data['Visit'])), key=lambda i: data['Visit'][i])
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visit_sorted = [data['Visit'][i] for i in sorted_indices]
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count_sorted = [data['patient_count'][i] for i in sorted_indices]
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# Re-plot with sorted x-axis:
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ax.clear()
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bars = ax.bar(visit_sorted, count_sorted, color='darkblue', label='Patients by Visit Count')
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# Re-apply labels, etc.
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ax.set_xlabel('Number of Visits', fontsize=12)
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ax.set_ylabel('Number of Unique Patients', fontsize=12)
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#ax.set_title('Number of Patients by Visit Number', fontsize=14)
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# Add legend
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ax.legend()
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# Improve layout and grid
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ax.grid(axis='y', linestyle='--', alpha=0.7)
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plt.xticks(visit_sorted) # Ensure all integer visit numbers are shown
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# Show the plot
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plt.tight_layout()
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plt.show()
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##
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# %% Patientjourney Bubble chart
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import matplotlib.pyplot as plt
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import numpy as np
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import matplotlib as mpl
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mpl.rcParams["font.family"] = "DejaVu Sans" # or "Arial", "Calibri", "Times New Roman", ...
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mpl.rcParams["font.size"] = 12 # default size for text
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mpl.rcParams["axes.titlesize"] = 14
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mpl.rcParams["axes.titleweight"] = "bold"
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# Data (your counts)
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visits = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9])
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patient_count = np.array([32, 24, 28, 17, 13, 6, 3, 3, 2])
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# "Remaining" = patients with >= that many visits (cumulative from the right)
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remaining = np.array([patient_count[i:].sum() for i in range(len(patient_count))])
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# --- Plot ---
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fig, ax = plt.subplots(figsize=(12, 3))
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y = 0.0 # all bubbles on one horizontal line
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# Horizontal line
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ax.hlines(y, visits.min() - 0.4, visits.max() + 0.4, color="#1f77b4", linewidth=3)
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# Bubble sizes (scale as needed)
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# (Matplotlib scatter uses area in points^2)
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sizes = patient_count * 35 # tweak this multiplier if you want bigger/smaller bubbles
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ax.scatter(visits, np.full_like(visits, y), s=sizes, color="#1f77b4", zorder=3)
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# Title
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#ax.set_title("Patient Journey by Visit Count", fontsize=14, pad=18)
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# Top labels: "1 visits", "2 visits", ...
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for x in visits:
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label = f"{x} visit" if x == 1 else f"{x} visits"
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ax.text(x, y + 0.18, label, ha="center", va="bottom", fontsize=10)
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# Bottom labels: "X patients" and "Y remaining"
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for x, pc, rem in zip(visits, patient_count, remaining):
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ax.text(x, y - 0.20, f"{pc} patients", ha="center", va="top", fontsize=9)
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ax.text(x, y - 0.32, f"{rem} remaining", ha="center", va="top", fontsize=9)
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# Cosmetics: remove axes, keep spacing nice
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ax.set_xlim(visits.min() - 0.6, visits.max() + 0.6)
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ax.set_ylim(-0.5, 0.35)
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ax.set_xticks([])
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ax.set_yticks([])
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for spine in ax.spines.values():
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spine.set_visible(False)
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plt.tight_layout()
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plt.show()
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plt.savefig("patient_journey.svg", format="svg", bbox_inches="tight")
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##
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