I have this line of code :

plot(gene_list$logFC, -log10(gene_list$P.Value),xlim=c(-10, 10), ylim=c(0, 15),xlab="log2 fold change", ylab="-log10 p-value")

which results in a volcano plot; however I want to find a way where I can color in red the points >log(2) and

Edit: Okay so as an example I'm trying to do the following to get a volcano plot:

install.packages("ggplot2")

and then

gene_list <- read.table("/Users/Javi/Desktop/gene_list.csv", header=T, sep=",")

require(ggplot2)
##Highlight genes that have an absolute fold change > 2 and a p-value <    0.05
gene_list$threshold = as.factor(abs(gene_list$logFC) > 2 & gene_list$P.Value < 0.05)

Construct the plot object

g = ggplot(data=gene_list, aes(x=logFC, y=-log10(P.Value),  colour=my_palette)) +
geom_point(alpha=0.4, size=5) +
theme(legend.position = "none") +
xlim(c(-10, 10)) + ylim(c(0, 15)) +
xlab("log2 fold change") + ylab("-log10 p-value")

What I want to do is to color the logFC values > 2 and in blue the logFC values < -2

You need to use the col argument, something like that should do it:

# first set up the plot
plot(gene_list$logFC, -log10(gene_list$P.Value),
     xlim=c(-10, 10), ylim=c(0, 15),
     xlab="log2 fold change", ylab="-log10 p-value",
     type="n")
# then add the points
sel <- which(gene_list$logFD<=log(2)) # or whatever you want to use
points(gene_list[sel,"logFC"], -log10(gene_list[sel,"P.value"]),col="black")
sel <- which(gene_list$logFD>log(2)) # or whatever you want to use
points(gene_list[sel,"logFC"], -log10(gene_list[sel,"P.value"]),col="red")