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)
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