Matlab is actually quite useful even for things as simple as plotting a file of data points. First you'll need a file with all the proper values. Let's say you have a file with all your data, arranged like this:
Let's additionally say that the name of the file is "test.dat". To load the data into matlab you would type the following at the matlab prompt:
Then "test" becomes a matrix where the first column is X and the second column is Y. To plot this, you can type:
Where "test(:,1)" means "the entire first column of matrix test".