r - 使用 R 的火山图中不同颜色的点

Question

这是一个简单的问题，我无法以某种方式获得所需的结果。我想构建一个火山图，我能够做到。这是代码:

CSCJFCTable <- read.table("volcano_plot_valuesCSCJ.csv", header = TRUE, sep = ",") 
with(CSCJFCTable, plot(log2.FC., -log10(raw.pval), pch=20, main=""))
abline(h = 1.0, col = "blue
", lty = 2, lwd = 1)
abline(v = c(-1,1), col = "blue
", lty = 2, lwd = 1)
with(subset(CSCJFCTable, X.log10.p.<1.0), points(log2.FC., -log10(raw.pval), pch=20, col="gray"))
with(subset(CSCJFCTable, abs(log2.FC.)>1), points(log2.FC., -log10(raw.pval), pch=20, col="orange"))

然后，这是结果图

我想把第一个盒子和第三个盒子里的点的颜色改成两种不同的颜色。所以，基本上，log2.FC. < -1 & -log10(raw.pval) > 1.0应该有一个颜色说红色和 log2.FC. > 1 & -log10(raw.pval) > 1.0应该有一个颜色绿色。并且，所有低于 -log10(raw.pval) = 1.0 的点都应该是灰色的。我怎样才能做到这一点？我厌倦了不同的组合，但它没有用。

Answer 1

我终于得到了想要的解决方案:

CSCJFCTable <- read.table("volcano_plot_valuesCSCJ.csv", header = TRUE, sep = ",") 
with(CSCJFCTable, plot(log2.FC., -log10(raw.pval), pch=20, main=""))
abline(h = 1.0, col = "blue
", lty = 2, lwd = 1)
abline(v = c(-1,1), col = "blue
", lty = 2, lwd = 1)
with(subset(CSCJFCTable, X.log10.p.<1.0), points(log2.FC., -log10(raw.pval), pch=20, col="gray"))
with(subset(CSCJFCTable, log2.FC.< -1 & X.log10.p.>1.0), points(log2.FC., -log10(raw.pval), pch=20, col="red"))


with(subset(CSCJFCTable, log2.FC.> 1 & X.log10.p.>1.0), points(log2.FC., -log10(raw.pval), pch=20, col="green"))