火山图

画第一张图

image.png

library(ggplot2)
library(ggrepel)
#library(ggsci)
library(dplyr)
#提取数据，resG是注释过基因名字的DEseq2结果
Vol.TG<-na.omit(resYvsM_order) 
#给结果加上change，其中padj和log2FoldChange后面的值根据自己的需要修改
Vol.TG$change <- as.factor(ifelse(Vol.TG$pvalue < 0.05 & abs(Vol.TG$log2FoldChange) > 1,ifelse(Vol.TG$log2FoldChange > 1,'UP','DOWN'),'NOT'))
#加个配色
#mypal_V = pal_gsea("default", n = 3, alpha = 0.9)(3)
#开始设置ggplot
#其中geom_point中alpha是点的透明度，size是点大小都可以修改。
#其中xlim是x轴范围，自己根据数据调整
#theme_bw中base_size是图中文字字号
#theme中那些事调整格子的，想知道效果删掉一个看一下。
#scale_color_manual中values后面值是配色，可以用c("","","")自己填颜色代号调整。limits代表change的顺序，这个要配合颜色顺序调整。
p <- ggplot(data = Vol.TG, aes(x = log2FoldChange, y = -log10(pvalue), color = change))+geom_point(alpha=0.8, size = 1)+scale_color_manual(values =c("blue","black","red"))+
geom_hline(yintercept = -log10(0.05),lty=4,lwd=0.6,alpha=0.8)+geom_vline(xintercept = c(1,-1),lty=4,lwd=0.6,alpha=0.8)+xlim(-9,9)+theme_bw(base_size = 18)+theme(panel.grid.minor = element_blank(),panel.grid.major = element_blank())
#输出p
p
#加上基因名，其中padj和log2FoldChange后面的值根据自己的需要修改
p+geom_text_repel(data=subset(data, abs(log2FoldChange) > 4.5), aes(label=row),col="black",alpha = 0.8)

画第二张图

image.png

##try drowing a volcano by gglot2
library(ggplot2)
library(ggrepel)
library(dplyr)
data <- resYvsM_order
data$significant <- as.factor(data$pvalue <0.05 & abs(data$log2FoldChange) > 1)
data$gene <- rownames(data)
ggplot(data=data, aes(x=log2FoldChange, y =-log10(pvalue),color=significant)) +
  geom_point(alpha=0.8, size=1.2)+
  scale_color_manual(values =c("black","red"))+
  labs(title="Volcanoplot", x="log2 (fold change)",y="-log10 (q-value)")+
  theme(plot.title = element_text(hjust = 0.4))+
  geom_hline(yintercept = -log10(0.05),lty=4,lwd=0.6,alpha=0.8)+
  geom_vline(xintercept = c(1,-1),lty=4,lwd=0.6,alpha=0.8)+
  #theme(legend.position='none')
  theme_bw()+
  theme(panel.border = element_blank(),
        panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(),   
        axis.line = element_line(colour = "black")) +
  #geom_text(aes(x=4,y=5,label="class is over"),col ="black",size = 10)+
  #geom_text(data=subset(data, abs(logFC) > 3), aes(label=gene),col="green",alpha = 0.5)
  geom_text_repel(data=subset(data, abs(log2FoldChange) > 8), aes(label=gene),col="black",alpha = 0.8)
#ggsave("vocanol.pdf",,width = 7.09, height =5.6,dpi = 300)