1、导入数据
import pandas as pd # Data analysis import numpy as np # Scientific computing import seaborn as sns # Statistical visualization # 读取数据 df = pd.read_csv('./dataset_volcano.txt', sep='\t') result = pd.DataFrame() result['x'] = df['logFC'] result['y'] = df['P.Value'] result['-log10(pvalue)']=-df['P.Value'].apply(np.log10)
2、设置阈值
# 设置pvalue和logFC的阈值 cut_off_pvalue = 0.0000001 cut_off_logFC = 1
3、设置分组
#分组为up, normal, down result.loc[(result.x> cut_off_logFC )&(result.y < cut_off_pvalue),'group'] = 'up' result.loc[(result.x< -cut_off_logFC )&(result.y < cut_off_pvalue),'group'] = 'down' result.loc[(result.x>=-cut_off_logFC )&(result.x<=cut_off_logFC )|(result.y >= cut_off_pvalue),'group'] = 'normal'
4、绘制散点图
#绘制散点图 ax = sns.scatterplot(x="x", y="-log10(pvalue)", hue='group', hue_order = ('down','normal','up'), palette=("#377EB8","grey","#E41A1C"), alpha=0.5, s=15,
5、设置散点图
#确定坐标轴显示范围 xmin=-6 xmax=10 ymin=7 ymax=13 ax.spines['right'].set_visible(False) #去掉右边框 ax.spines['top'].set_visible(False) #去掉上边框 ax.vlines(-cut_off_logFC, ymin, ymax, color='dimgrey',linestyle='dashed', linewidth=1) #画竖直线 ax.vlines(cut_off_logFC, ymin, ymax, color='dimgrey',linestyle='dashed', linewidth=1) #画竖直线 ax.hlines(-np.log10(cut_off_pvalue), xmin, xmax, color='dimgrey',linestyle='dashed', linewidth=1) #画竖水平线 ax.set_xticks(range(xmin, xmax, 4))# 设置x轴刻度 ax.set_yticks(range(ymin, ymax, 2))# 设置y轴刻度 ax.set_ylabel('-log10(pvalue)',fontweight='bold') # 设置y轴标签 ax.set_xlabel('log2(fold change)',fontweight='bold') # 设置x轴标签
以上就是python中画火山图的方法,希望能对大家有所帮助,更多知识尽在python教程网。
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