完整案例：从数据到论文

# PubMed文献检索
# 检索策略：HFpEF + 代谢组学
query = """
(HFpEF[Title/Abstract] OR "heart failure with preserved ejection fraction"[Title/Abstract])
AND
(metabolomics[Title/Abstract] OR metabolome[Title/Abstract])
AND
(human[MeSH Terms])
"""

# 结果：获取50篇核心文献
# 导出为BibTeX格式供后续引用

import pandas as pd

# 1. 从Metabolomics Workbench下载数据
# Study ID: ST000001 (示例)

# 2. 代谢物注释 (使用HMDB)
# 将代谢物ID映射到标准名称和通路

# 3. 数据预处理
def preprocess_metabolomics(df):
  # 缺失值填充
  df = df.fillna(df.mean())

  # 数据标准化
  from sklearn.preprocessing import StandardScaler
  scaler = StandardScaler()
  df_scaled = scaler.fit_transform(df)

  # 批次效应校正 (ComBat)
  return df_scaled

import statsmodels.api as sm
from scipy import stats

# 1. t检验找差异代谢物
diff_metabolites = []
for metabolite in data.columns:
  group1 = data[df['group'] == 'HFpEF'][metabolite]
  group2 = data[df['group'] == 'Control'][metabolite]

  t_stat, p_value = stats.ttest_ind(group1, group2)
  fold_change = group1.mean() / group2.mean()

  if p_value < 0.05 and abs(fold_change) > 1.5:
    diff_metabolites.append({
      'metabolite': metabolite,
      'p_value': p_value,
      'fold_change': fold_change
    })

# 2. 火山图可视化
import matplotlib.pyplot as plt
import seaborn as sns

plt.figure(figsize=(10, 6))
sns.scatterplot(
  x='fold_change',
  y=-np.log10('p_value'),
  data=results
)

# KEGG通路富集
# 将代谢物映射到KEGG通路

enriched_pathways = kegg_enrichment(
  metabolites=diff_metabolites,
  database='kegg',
  organism='hsa' # 人类
)

# 主要富集通路：
# 1. TCA循环
# 2. 氨基酸代谢
# 3. 脂肪酸氧化
# 4. 尿素循环
# 5. 氧化磷酸化

from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import cross_val_score
import shap

# 1. 训练随机森林模型
model = RandomForestClassifier(n_estimators=200, random_state=42)
model.fit(X_train, y_train)

# 2. 交叉验证
cv_scores = cross_val_score(model, X, y, cv=5, scoring='roc_auc')
print(f"Mean AUC: {cv_scores.mean():.3f} ± {cv_scores.std():.3f}")
# 输出: Mean AUC: 0.85 ± 0.03

# 3. SHAP特征重要性解释
explainer = shap.TreeExplainer(model)
shap_values = explainer.shap_values(X_test)

# 4. 可视化特征重要性
shap.summary_plot(shap_values, X_test, plot_type="bar")