Reduce PDF file size of plots by filtering hidden objects

As a start you can do something like this:

set.seed(42)
DF <- data.frame(x=x<-runif(1e6),y=x+rnorm(1e6,sd=0.1))
plot(y~x,data=DF,pch=".",cex=4)

PDF size: 6334 KB

DF2 <- data.frame(x=round(DF$x,3),y=round(DF$y,3))
DF2 <- DF[!duplicated(DF2),]
nrow(DF2)
#[1] 373429
plot(y~x,data=DF2,pch=".",cex=4)

PDF size: 2373 KB

With the rounding you can control how many values you want to remove. You only need to modify this to handle the different colours.