R软件-ggplot2 画火山图

R软件

ggplot2

1 导入包

# 帮助文档链接：http://docs.ggplot2.org/current/

library(ggplot2)

 

2.改变工作路径，将工作路径改变到数据存放的文件夹下

3.读取数据：isoforms.filter.tsv

isoforms.filter.tsv表格内容：

id R0_count R3_count R0_fpkm R3_fpkm log2FC Pvalue FDR significant

OS01T0100100-01 234.00 199.00 2.90 2.66 -0.124626654513745 0.365789357378185 0.524535855815267 no

OS01T0100200-01 21.00 31.00 0.80 1.28 0.678071905112638 0.126839251293283 0.222003795467898 no

OS01T0100300-00 1.00   0.00 0.06 0.001 -5.90689059560852 1 1 no

OS01T0100400-01 56.00 123.00 0.98 2.31 1.23703919730085 3.93302992478971e-08 2.24773679121402e-07 up

OS01T0100466-00 0.00 2.00 0.001 0.09 6.49185309632967 0.50002499875013 0.653216704283588 no

OS01T0100500-01 323.00 412.00 5.46 7.50 0.457989644463391 3.59555466153389e-05 0.000144630279061904 no

OS01T0100600-01 95.00 83.00 1.85 1.75 -0.0801703486839833 0.709182152567053 0.84908871394211 no

 

data =read.table("isoforms.filter.tsv",header=T,row.names=1)

4. 画图

r03 = ggplot(data,aes(log2FC,-1*log10(FDR)))

 

r03 + geom_point()

                                                 

4.1 改变点的颜色

r03 + geom_point(color ="red")

r03 +geom_point(aes(color ="red"))

r03 + geom_point(aes(color =significant))

                                               

4.2 设置坐标轴范围和标题 # xlim()，ylim()函数，labs(title=“..”,x=“..”,y=“..”)函数

r03xy = r03 +geom_point(aes(color =significant)) + xlim(-4,4) + ylim(0,30)

r03xy + labs(title="Volcanoplot",x="log2(FC)")

r03xy + labs(title="Volcanoplot",x=expression_r(log[2](FC)), y=expression_r(-log[10](FDR)))

4.3 自定义颜色

r03xyp = r03xy + labs(title="Volcanoplot",x=expression_r(log[2](FC)), y=expression_r(-log[10](FDR)))

r03xyp + scale_color_manual(values =c("green","black", "red"))

volcano = r03xyp +scale_color_manual(values = c("#00ba38","#619cff","#f8766d"))

 

4.4 添加阈值线

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)

5.保存图片

ggsave("volcano.png")

 

ggsave("volcano8.png",volcano,width=8,height=8)