火山(Volcano Plot)图在一张图中显示了两个重要的指标(Fold change/pvalue),可以非常直观且合理地筛选出在两样本间发生差异表达的基因。检验分析出两样本间显著差异表达的基因后,以log2(fold change)为横坐标,以T检验显著性检验P值的负对数-log10(pvalue)为纵坐标,即可得火山图(Volcano Plot)。
> install.packages("ggplot2")
> library(ggplot2)
> R0_vs_R3_isoforms_fitter <- read_excel("~/Downloads/R0-vs-R3.isoforms.fitter.xlsx")
> data <- R0_vs_R3_isoforms_fitter
> r03 <-ggplot(data,aes(log2FC,-1*log10(FDR)))
> r03 + geom_point()
运行过程数据及图片:
改变点的颜色:
> r03 + geom_point(color="red")
> r03 + geom_point(aes(color="red"))
> r03 + geom_point(aes(color=significant))
设置标题,坐标轴范围
>r03+geom_point(aes(color=significant))+xlim(-4,4)+ylim(0,30)
>r03xy=r03+geom_point(aes(color=significant))+xlim(-4,4)+ylim(0,30)
> r03xy + labs(title="Volcano plot",x="log2(FC)")
> r03xy + labs(title="Volcanoplot",x=expression(log[2](FC),y=expression(-log[10](FDR))))
自定义颜色
> r03xy + labs(title="Volcanoplot",x=expression(log[2](FC),y=expression(-log[10](FDR))))
> r03xyc = r03xy+labs(title="Volcanoplot",x=expression(log[2](FC)), y=expression(-log[10](FDR)))
> r03xyc + scale_color_manual(values =c("green","black", "red"))
>r03xyc + scale_color_manual(values =c("green","blue", "red"))
> volcano = r03xyc +scale_color_manual(values = c("green","blue","red"))
>volcano+geom_hline(yintercept=1.3)+geom_vline(xintercept=c(-1,1))
>volcano+geom_hline(yintercept=1.3,linetype=4)+geom_vline(xintercept=c(-1,1),linetype=4)
保存图片:
>ggsave("volcano.png")
>ggsave("volcano8.png",volcano,width=8,height=8)
好吧,学习使人疯狂,脑袋疼学起画图一样起劲的忘休息。