That is closer, thank you. I needed the par command. Although, it still does not differentiate classes.

I can, however, now do so by:

plot(x4~x1, pch=10, col=r)

par(new=T)

plot(x4~x1,pch=12, col=!r)

this works great to separate the two classes

(i.e. one pch=10 for r=1, pch=12 for r=0).

The only problem is I lose color attributes, and

do not know enough to add the additional color attribute to col=r, cannot just add col=r, col='red' and also tried to create a vector att<- c(r,'red') which only worked for 1 dot.

Much closer though.

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edit: manual way to do it.

If you know the count of classes, then

let c0 = count(r such that c=0)

let c1 = count(r such that c=1)

then create vector:

cv <- c(rep("red",c0), rep("blue",c1),r)

then plot as follows,

plot(x4 ~ x1, pch=12, col=cv)

works like a charm...

only you have to count instances of each class.