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近日在《The new england journal o f medicine》杂志看到一篇文章的图，如下，这种图应该是用GraphPad prism做的，图的特点是散点统计图，仔细观察中间还展示了平均值和四分位数，坐标轴也是截断的。这里我们使用R来做一下。 （Reference：A Novel Circulating MicroRNA
for the Detection of Acute Myocarditis）
示例数据及注释代码已上传群文件！ 首先读入数据，包含表达值和分组：
setwd("E:/生物信息学/ggplot坐标轴截断")A <- read.csv("Exp.csv", header = T)library(ggplot2)library(forcats)library(ggpubr)A$GeneSymbol <- as.factor(A$GeneSymbol)A$GeneSymbol <- fct_inorder(A$GeneSymbol)
计算四分位数：
B <- A %>% group_by(GeneSymbol) %>% mutate(upper = quantile(S100A12, 0.75), lower = quantile(S100A12, 0.25), mean = mean(S100A12), median = median(S100A12))
设置需要比较的分组：
my_comparisons1 <- list(c("Asymptomatic", "Mild")) my_comparisons2 <- list(c("Asymptomatic", "Severe"))my_comparisons3 <- list(c("Asymptomatic", "Critical"))
ggplot作图：
p <- ggplot(A, aes(GeneSymbol, S100A12, shape=GeneSymbol, fill=GeneSymbol))+ geom_jitter(size=3, position = position_jitter(0.2))+ scale_shape_manual(values = c(21,24,25,22))+ scale_fill_manual(values=c("grey", "#0073B5", "#C9543B", "#E59F3F"))+ geom_errorbar(data=B, aes(ymin = lower, ymax = upper),width = 0.2,size=0.5)+ stat_summary(fun = "mean", geom = "crossbar", mapping = aes(ymin=..y..,ymax=..y..), width=0.4, size=0.3)+ theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.line=element_line(colour="black"), axis.title.x = element_blank(), axis.title.y = element_blank(), axis.text.x = element_text(size = 14,angle = 45, vjust = 1,hjust = 1, color = 'black',face="bold"), axis.text.y = element_text(size = 12, color = 'black'), plot.title = element_text(hjust = 0.5,size=15,face="bold"), legend.position = "NA")+ ggtitle("S100A2")+ stat_compare_means(method="t.test",hide.ns = F, comparisons =c(my_comparisons1,my_comparisons2,my_comparisons3), label="p.signif", bracket.size=0.8, size=6)
坐标轴截断，有很多函数可以实现，这里演示两种：
install.packages("gg.gap")library(gg.gap)gg.gap(plot=p, segments=c(5,10), ylim=c(0,850), tick_width = c(1,100))
还有ggbreak： install.packages("ggbreak")library(ggbreak)
p+scale_y_cut(breaks = 5, which = c(1,3), scales = c(3,0.5), space = 0.1)
总体可以，像文章中的要做很多数据的时候，可以使用循环作图。当然了，一般情况还是建议用prism做就可以了，因为还是比较方便！
看完了。觉得分享有用的话，帮忙点个赞，分享一下再走呗！
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