我从tcga下载了表达矩阵跟临床数据,怎么画km曲线,帮我写一串代码
时间: 2024-12-13 22:19:33 浏览: 12
要在Python中利用scikit-survival库绘制Kaplan-Meier (KM) 曲线,你需要按照以下步骤操作:
首先,确保已经安装了`pandas`, `numpy`, `scipy`, `matplotlib`, 和 `sksurv` 这些库。如果没有安装,可以使用pip安装:
```bash
pip install pandas numpy scipy matplotlib scikit-surv
```
假设你的表达矩阵是一个CSV文件(如`expression.csv`),临床数据在一个CSV文件(如`clinical_data.csv`),并且`Survival`列包含生存时间,`Status`列包含是否 censoring的信息:
1. 导入所需的库并加载数据:
```python
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from sksurv.datasets import load_tcgagene
from sksurv.plotting import kaplan_meier_estimator
import matplotlib.pyplot as plt
# 加载表达矩阵
expression_df = pd.read_csv('expression.csv', index_col=0)
# 加载临床数据
clinical_df = pd.read_csv('clinical_data.csv')
```
2. 将临床信息合并到表达矩阵:
```python
data = expression_df.merge(clinical_df, left_index=True, right_index=True)
X = data.drop(['Survival', 'Status'], axis=1)
y = data['Survival'].astype(float)
censoring = data['Status'] == 1
```
3. 划分训练集和测试集:
```python
X_train, X_test, y_train, y_test, event_train, event_test = train_test_split(X, y, censoring, test_size=0.2, random_state=42)
```
4. 绘制KM曲线:
```python
# 对于特定的特征或所有特征都可以绘制
feature_of_interest = 'feature_column_name' # 请替换为实际的特征名称
kmf = KaplanMeierFitter()
kmf.fit(y_train, event_train, label=feature_of_interest)
# 绘制
plt.figure(figsize=(8, 6))
ax = kmf.plot(ax=plt.gca(), ci_show=False)
ax.set_xlabel('Time (months)')
ax.set_ylabel('Survival probability')
ax.set_title(f'Kaplan-Meier curve for {feature_of_interest}')
plt.show()
```
阅读全文