复现GMM文章（二）：图2代码和数据

介绍

复现GMM文章的的Fig2图。

加载R包

  library(tidyr)
  library(tidyverse)
  library(dplyr)
  library(ggsci)
  library(ggpubr)

导入数据

所有的数据可以通过下列链接下载：

百度网盘链接: https://pan.baidu.com/s/1isKEK1G5I6X90KYqLufmWw

提取码: t9ca

图2A

• 数据

load('01_data/plot_data/F2A.RData')

stat.test <- compare_means(
  auc~group1,data = auc_external,
  method = "wilcox.test") %>% 
  mutate(y.position = seq(from=1.15, to=1.9,length.out=10))
x <- stat.test$p.adj
stat.test$p.adj.signif<-ifelse(x<0.05, ifelse(x<0.01, ifelse(x<0.001, ifelse(x<=0.0001, '****','***'),'**'),'*'),'ns')

• 画图

p1 <- ggviolin(auc_external, x = "group1", y = "auc", fill = "group1",alpha = 0.3,
               palette = "jco",add = "boxplot",width = 0.6)+
  geom_hline(yintercept =0.5,color='#dbdcdc')+
  geom_hline(yintercept =0.6,color='#ffd09a')+
  geom_hline(yintercept =0.7,color='#ffcbd8')+
  geom_hline(yintercept =0.8,color='#7b77ff')+
  # stat_compare_means()+
  ylim(0.05,1.9)+
  theme(legend.position="none")+   
  xlab("") + ylab("External AUC")+
  ggtitle("Disease category")+
  theme(axis.text.x=element_text(angle=20, hjust=0.8,face = 'plain',size=13),
        text = element_text(size=13,face = 'plain',family ='',colour = 'black')) + 
  stat_pvalue_manual(stat.test,label = "p.adj.signif")

p1

图2B

• 数据

load('01_data/plot_data/F2B.RData')

head(self.e)

stat.test <- compare_means(
  auc~level,data = self.e, 
  # group.by = "level",
  method = "wilcox.test") %>% 
  mutate(y.position = seq(from=1.35, to=1.7,length.out=3))
x <- stat.test$p.adj
stat.test$p.adj.signif <- ifelse(x<0.05, ifelse(x<0.01, ifelse(x<0.001, ifelse(x<=0.0001, '****','***'),'**'),'*'),'ns')

• 画图

p2 <- ggviolin(self.e, x = "level", y = "auc", fill = "level",alpha = 0.3,
           palette = c('#774ec7','#bd93cc','#a2c4b1'),add = "boxplot",width = 0.5)+
  geom_hline(yintercept =0.5,color='#dbdcdc')+
  geom_hline(yintercept =0.6,color='#ffd09a')+
  geom_hline(yintercept =0.7,color='#ffcbd8')+
  geom_hline(yintercept =0.8,color='#7b77ff')+
  ylim(0.05,1.9)+
  # stat_compare_means()+
  theme(legend.position="none")+    
  ylab("External AUC")+xlab('')+
  ggtitle('Data type')+
  theme(axis.text.x=element_text(angle=20, hjust=0.8,face = 'plain',size=13),
        text = element_text(size=13,face = 'plain',family ='',colour = 'black')) +
  stat_pvalue_manual(stat.test,label = "p.adj.signif")

p2

图2C

• 数据

load('01_data/plot_data/F2C.RData')

head(self.e)

stat.test <- compare_means(
  auc~group1,data = self.e, group.by = "level",
  method = "wilcox.test") %>% 
  mutate(y.position = c(seq(from=1, to=1.5,length.out=10),rep(seq(from=1, to=1.3,length.out=6), times=2)))
x <- stat.test$p.adj
stat.test$p.adj.signif <- ifelse(x<0.05, ifelse(x<0.01, ifelse(x<0.001, ifelse(x<=0.0001, '****','***'),'**'),'*'),'ns')

• 画图

p3 <- ggboxplot(self.e, x = "group1", y = "auc",color = "group1", palette = "jco", add = "jitter",
               width = 0.5,add.params = list(size=1))+
  facet_wrap(vars(level),scales = "free")+
  stat_compare_means(aes(label = paste0('p = ',..p.format..)),label.y = 1.5,hjust=-0.01)+
  theme(axis.text.x = element_blank(),axis.ticks=element_blank(),legend.position="none")+ 
  xlab("Disease category") + ylab("External AUC")+
  labs(color = "disease type")+
  theme(text = element_text(size=13,face = 'plain',family ='',colour = 'black')) + 
  stat_pvalue_manual(stat.test,label = "p.adj.signif")

p3

图2D

• 数据

load('01_data/plot_data/F2D.RData')

head(self.e)

stat.test <- compare_means(
  auc~level,data = self.e, group.by = "subtype",
  method = "wilcox.test") %>% 
  mutate(y.position = rep(seq(from=1, to=1.15,length.out=3), times=4))
x <- stat.test$p.adj
stat.test$p.adj.signif <- ifelse(x<0.05, ifelse(x<0.01, ifelse(x<0.001, ifelse(x<=0.0001, '****','***'),'**'),'*'),'ns')

• 画图

p4 <- ggboxplot(self.e, x = "level", y = "auc",color = "level", add = "jitter",
               palette = c('#774ec7','#bd93cc','#a2c4b1'),
               width = 0.5,add.params = list(size=1))+
  facet_wrap(vars(subtype),nrow = 1)+
  stat_compare_means(aes(label = paste0('p = ',..p.format..)),label.y = 1.25,hjust=-0.01)+
  theme(axis.text.x = element_blank(),axis.ticks=element_blank(),legend.position="none")+
  xlab("Data type") + ylab("External AUC")+
  theme(text = element_text(size=13,face = 'plain',family ='',colour = 'black')) + 
  stat_pvalue_manual(stat.test,label = "p.adj.signif")

p4