ggplot2:火山图

火山图是散点图的一种,也是描点,用 geom_point()绘图

1.加载包,读入数据及数据格式

library(ggplot2)
data = read.table("R0-vsR3.isoforms.filter.tsv",header=T,row.names=1)

2.绘图

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

3.改变点的颜色

r03 + geom_point(color="red")
r03 + geom_point(aes(color="red"))
r03 + geom_point(aes(color=significant)) # 按照“ significant”这一列定义点的颜色;

4.设置坐标轴范围和标题

函数xlim(),ylim(),规定X、 Y轴范围;labs(title=“..”,x=“..”,y=“..”),确定标题和坐标轴标签;expression函数改变样式,[]是用来添加下标,^是用来添加上标

r03xy = r03 + geom_point(aes(color=significant)) + xlim(-4,4) + ylim(0,30)
r03xy + labs(title="Volcano plot",x="log2(FC)")
r03xy + labs(title="Volcano plot",x=expression(log[2](FC)),y=expression(-log[10](FDR)))

5.自定义颜色

scale_color_manual(): 自定义颜色配色;

r03xyp = r03xy + labs(title="Volcano plot",x=expression(log[2](FC)),y=expression(-log[10](FDR)))
r03xyp + scale_color_manual(values = c("green","black", "red"))
volcano = r03xyp + scale_color_manual(values = c("#00ba38","#619cff", "#f8766d"))

6.添加阈值线

geom_hline()添加水平线; geom_vline()添加垂直线

volcano+geom_hline(yintercept=1.3)+geom_vline(xintercept=c(-1,1))

7.改变线条类型

linetype参数0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash

volcano+geom_hline(yintercept=1.3,linetype=4)+geom_vline(xintercept=c(-1,1),linetype=4)

详细讲解查看帮助文档基迪奥在线视频


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