You need to be more clear about your question....
shown_graph = zeros(length(x),length(y));
%plotting points into graph
[xpoint ypoint] = find(shown_graph == 0);
scatter(xpoint,ypoint,100,'.');
The above lines are meaning less, you have intiated shown_graph as all zeros, and obviously when you seek zeros, you will get all the points. What exactly you are trying?