绘制GSVA基因集的火山图

rm(list = ls()) 
#load(file = "step1output.Rdata")
load(file = "step4output.Rdata")
#1.火山图----
library(dplyr)
library(ggplot2)
library(ggrepel)
dat  = deg
head(dat)
write.csv(dat,'dat.csv')
#方法1
#step1:先把图画出来


p <-ggplot(data = dat, 
            aes(x = logFC, 
                y = -log10(P.Value)
                ))+
  geom_point(alpha=0.4, size=3.5, 
             aes(color=change))+
  ylab("-log10(p_val)")+
  scale_color_manual(values=c("blue", "grey","red"))+
  geom_vline(xintercept=c(-logFC_t,logFC_t),lty=4,col="black",lwd=0.8)+
  geom_hline(yintercept = -log10(P.Value_t),lty=4,col="black",lwd=0.8)+
  theme_bw()
p
# step2:筛选部分基因，用于显示在图上
# 想在图上做修改，一半是调参数，一半是调数据。我们现在要做的就是调数据：要标记的，label=基因，无需标记的，label=“”。
dat$label=ifelse(dat$P.Value < 0.05 & abs(dat$logFC) >= 0,dat$symbol,'')
p1 <- p+geom_text_repel(data = dat, aes(x = logFC ,
                                     y = -log10(P.Value), 
                                     label = label),
                    size = 3,box.padding = unit(0.5, "lines"),
                    point.padding = unit(0.8, "lines"), 
                    segment.color = "black", 
                    show.legend = FALSE)