I decided to go with circles instead of rectangles. Thank you for your help.
Here is the new code:

dev.new(width=2.5, height=3,mar=c(0,0,0,0))
par(mfrow=c(1,1),mar=c(0,0,0,0))
x=c(-1,1,1,-1,-3,-3,5)
y=c(1.2,0.6,-.7,-1.3,-.7,0.6,5)
plot(0,xlim=c(-4,2),ylim=c(-2,2),type="n",axes=FALSE,xlab="",ylab="") 
symbols(x,y,circles=c(1,1,1,1,1,1,4), 
 
bg=c("brown","blue","orange","red","yellow","green","white"),fg="white",add=TRUE)
 


I added in the "white" one because that makes all the circles smaller. I
tried changing the radii of the circles, but it seems they are relative so I
made a white one big and the rest small.

-----
In theory, practice and theory are the same. In practice, they are not - Albert 
Einstein
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