介绍
附图2代码
导入R包
library(tidyverse)
library(ggpubr)
library(ggplot2)
library(ggrepel)
library(patchwork)
Figure S2A
load('01_data/plot_data/FS2A.RData')
stat.test <- compare_means(
auprc~group1,data = auc_self,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.05, to=1.65,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')
p1 <- ggboxplot(auc_self, x = "group1", y = "auprc", fill = "group1",
palette = "jco",width = 0.2)+
theme_bw() +
ylim(0.15,1.68)+
theme(legend.position="none")+
ylab("Internal AUPRC")+xlab('')+
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
load('01_data/plot_data/F1E.RData')
stat.test <- compare_means(
auprc~level,data = self.e,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.2, to=1.65,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')
p2 <- ggboxplot(self.e, x = "level", y = "auprc", fill = "level",
width = 0.2,palette = c('#774ec7','#bd93cc','#a2c4b1'))+
theme_bw() +
ylim(0.15,1.68)+
theme(legend.position="none")+
ylab("Internal AUPRC")+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
pA <- ggarrange(p1,p2,
ncol = 2, nrow = 1,
widths = c(4,3))
pA
Figure S2B
load('01_data/plot_data/FS2B.RData')
stat.test <- compare_means(
auprc~group1,data = auc_self,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.05, to=1.65,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')
p1 <- ggboxplot(auc_self, x = "group1", y = "auprc", fill = "group1",
palette = "jco",width = 0.2)+
theme_bw() +
ylim(0.15,1.68)+
theme(legend.position="none")+
ylab("External AUPRC")+xlab('')+
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
load('01_data/plot_data/F1E.RData')
stat.test <- compare_means(
auprc~level,data = self.e,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.2, to=1.65,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')
p2 <- ggboxplot(self.e, x = "level", y = "auprc", fill = "level",
width = 0.2,palette = c('#774ec7','#bd93cc','#a2c4b1'))+
theme_bw() +
ylim(0.15,1.68)+
theme(legend.position="none")+
ylab("External AUPRC")+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
pB <- ggarrange(p1,p2,
ncol = 2, nrow = 1,
widths = c(4,3))
pB
Figure S2C
load('01_data/plot_data/FS2C.RData')
stat.test <- compare_means(
mcc~group1,data = auc_self,
method = "wilcox.test") %>%
mutate(y.position = seq(from=0.9, to=1.65,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')
p1 <- ggboxplot(auc_self, x = "group1", y = "mcc", fill = "group1",
palette = "jco",width = 0.2)+
ylab("Internal MCC")+xlab('')+
ggtitle('Disease category')+
theme_bw() +
theme(legend.position="none")+
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
load('01_data/plot_data/F1E.RData')
stat.test <- compare_means(
mcc~level,data = self.e,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.2, to=1.65,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')
p2 <- ggboxplot(self.e, x = "level", y = "mcc", fill = "level",
width = 0.2,palette = c('#774ec7','#bd93cc','#a2c4b1'))+
theme_bw() +
theme(legend.position="none")+
ylab("Internal MCC")+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
pC <- ggarrange(p1,p2,
ncol = 2, nrow = 1,
widths = c(4,3))
pC
Figure S2D
load('01_data/plot_data/FS2D.RData')
stat.test <- compare_means(
mcc~group1,data = auc_self,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=0.9, to=1.65,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')
p1 <- ggboxplot(auc_self, x = "group1", y = "mcc", fill = "group1",
palette = "jco",width = 0.2)+
ylab("External MCC")+xlab('')+
ggtitle('Disease category')+
theme_bw() +
theme(legend.position="none")+
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
load('01_data/plot_data/F1E.RData')
stat.test <- compare_means(
mcc~level,data = self.e,
# group.by = "level",
method = "wilcox.test") %>%
mutate(y.position = seq(from=1.2, to=1.65,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')
p2 <- ggboxplot(self.e, x = "level", y = "mcc", fill = "level",
width = 0.2,palette = c('#774ec7','#bd93cc','#a2c4b1'))+
theme_bw() +
theme(legend.position="none")+
ylab("External MCC")+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
pD <- ggarrange(p1,p2,
ncol = 2, nrow = 1,
widths = c(4,3))
pD
