火山图绘制

#第一步
temp<-read.csv('mapp.csv',header=TRUE,row=1)
head(temp)
#第二步
temp$change <- as.factor(ifelse(temp$p < 0.01 & abs(temp$fc) > 1,ifelse(temp$fc > 1,'DOWN','UP'),'NOT'))#新增改列，利用ifelse函数添加基因的上下调情况，color进行区分，然后使用geom_hline（）和geom_vline（）参数添加阈值线，

temp$sign <- ifelse(temp$p < 1.0e-60 & abs(temp$fc) > 3.9,rownames(temp),NA)  #新增注册列，利用ifelse函数添加重点显着差异基因，然后使用geom_text参数添加到图上，
library("ggplot2")


第三步
#p1 带文字的
p1 <- ggplot(temp, aes(x =fc, y =-log10(q),color = change)) +
  geom_point(size = 1.1,alpha=0.5) +
  geom_vline(xintercept = c(-1, 1), lty = 4,color="black") + 
  geom_hline(yintercept = c(-2, 2), lty = 4,color="black") +
  theme_bw()+
  scale_color_manual(name = "", values = c("red", "blue", "black"), limits = c("UP", "DOWN", "NOT"))+#设置不同颜色
  geom_text(aes(label = sign), size = 4,color="black") +#设置文字
  labs(x = 'log2 Fold Change', y = '-log10 q-value')

p1


#p2 代标签框的
library(ggrepel)
p2 <- ggplot(temp, aes(x =fc, y =-log10(q),color = change)) +
  geom_point(size = 2,alpha=0.7) +
  geom_vline(xintercept = c(-1, 1), lty = 4,color="black") + 
  geom_hline(yintercept = c(-2, 2), lty = 4,color="black") +
  theme(panel.grid = element_blank(), panel.background = element_rect(color = 'black', fill = 'transparent'))+
  scale_color_manual(name = "", values = c("red", "blue", "gray"), limits = c("UP", "DOWN", "NOT"))+
  labs(x = 'log2 Fold Change', y = '-log10 q-value')+
  geom_label_repel(aes(label=sign), fontface="bold",color="black", box.padding=unit(0.35, "lines"))#设置文本框

p2

image.png 4b876a8e21b060f6e6ca5d42bf6f1a8.jpg