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You need a new plot window, and also a coordinate system, so you need plot.new() and plot.window(), then you can start to add graph elements:
plot.new()
plot.window()
plot.new( ) plot.window( xlim=c(-5,5), ylim=c(-5,5) ) points( rnorm(100), rnorm(100) ) axis( side=1 )
example plot