❝本节来介绍如何使用ggplot2来绘制森林图，下面通过一个小例子来进行展示 ❞
加载R包
代码语言：javascript复制library(tidyverse)
导入数据
代码语言：javascript复制unicox <- read_csv("AKT3_mRNA_OS_pancan_unicox.csv")
绘制森林图
代码语言：javascript复制p1 <- ggplot(unicox,aes(HR_log, cancer, col=Type))
geom_point(aes(size=-log10(p.value)))
geom_errorbarh(aes(xmax =upper_95_log, xmin = lower_95_log), height = 0.4)
scale_x_continuous(limits= c(-2, 2), breaks= seq(-1, 1, 1))
geom_vline(aes(xintercept = 0))
xlab('HR(95%CI)') ylab(' ')
theme_bw(base_size = 12)
theme(axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.text.x=element_text(color="black"),
axis.title.y=element_blank(),
plot.margin = unit(rep(0,4),"cm"),
legend.title = element_blank(),
legend.key=element_blank(), # 图例键为空
legend.text = element_text(color="black",size=9), # 定义图例文本
legend.spacing.x=unit(0.1,'cm'), # 定义文本书平距离
legend.spacing.y=unit(0.1,'cm'),
legend.key.width=unit(0.2,'cm'), # 定义图例水平大小
legend.key.height=unit(0.2,'cm'), # 定义图例垂直大小
legend.background=element_blank(), # 设置背景为空
legend.box.background=element_rect(colour="black"), # 图例绘制边框
legend.position=c(1,0),legend.justification=c(1,0))
scale_color_manual(values = c("gray", "steelblue", "red"))
绘制基因名称
代码语言：javascript复制p2 <- unicox %>% select(cancer) %>% distinct() %>% mutate(group="A") %>%
ggplot(aes(group,cancer))
geom_text(aes(group,cancer,label=cancer ),size=3,color="black")
geom_stripped_rows()
theme(panel.grid.major = element_blank(),
axis.text=element_blank(),
axis.ticks = element_blank(),
axis.title.y=element_blank(),
plot.margin = unit(rep(0,4),"cm"))
labs(x="Gene")
scale_x_discrete(position = "top")
展示置信区间
代码语言：javascript复制p3 <- unicox %>% select(6,7,8) %>% mutate(across(where(is.numeric),~round(.,2))) %>%
mutate(`HR(95%Cl)`=paste(HR_log,"[",lower_95_log," to ",upper_95_log,"]",sep="")) %>% select(4) %>%
mutate(group="HR(95%Cl)") %>%
ggplot(aes(group,`HR(95%Cl)`))
geom_text(aes(group,`HR(95%Cl)`,label=`HR(95%Cl)`),size=3,color="black")
geom_stripped_rows()
theme(panel.grid.major = element_blank(),
axis.text=element_blank(),
axis.ticks = element_blank(),
axis.title.y=element_blank(),
plot.margin = unit(rep(0,4),"cm"))
labs(x="HR(95%Cl)")
scale_x_discrete(position = "top")
展示pvalue
代码语言：javascript复制p4 <- unicox %>% select(p.value) %>%
mutate(across(where(is.numeric),~round(.,2))) %>%
mutate(group="A",p.value=as.character(p.value)) %>%
ggplot(aes(group,p.value))
geom_text(aes(group,p.value,label=p.value),size=3,color="black")
geom_stripped_rows()
theme(panel.grid.major = element_blank(),
axis.text=element_blank(),
axis.ticks = element_blank(),
axis.title.y=element_blank(),
plot.margin = unit(rep(0,4),"cm"))
labs(x="p.value")
scale_x_discrete(position = "top")
拼图
代码语言：javascript复制library(patchwork)
(p2 p3 p4 p1) plot_layout(widths = c(.12,0.28,.15,.8))
