As far as I undertood your question, this could be helpful
> set.seed(1)
> big.file <- matrix(rnorm(1e3, 100, 3), ncol=2) # simulating your big data
>
>
> # choosing 1% randomly
> one.percent <- big.file[sample(1:nrow(big.file), 0.01*nrow(big.file)), ]
[,1] [,2]
[1,] 99.40541 106.50735
[2,] 98.44774 98.53949
[3,] 101.50289 102.74602
[4,] 96.24013 104.97964
[5,] 101.67546 102.30483
Then you can plot it
> plot(one.percent)