If you want to show how your plots change with time, a movie is a good idea. Especially since MATLAB can produce movies that can be embedded in your presentations, or be seen with any good ol' movie player. Here's how:

The idea is to create plot figures and compile them as frames of your movie.

% Create a new figure, and position it
    fig1 = figure;
    winsize = get(fig1,'Position');
    winsize(1:2) = [0 0];
% Create movie file with required parameters
    fps= 25;
    outfile = sprintf('%s',outFileName)
    mov = avifile(outfile,'fps',fps,'quality',100);
% Ensure each frame is of the same size
    set(fig1,'NextPlot','replacechildren');
    for i=1:numframes
        plot(x,y); % generate your plot
% put this plot in a movieframe
% In case plot title and axes area are needed
%       F = getframe(fig1,winsize);
% For clean plot without title and axes
        F = getframe;
        mov = addframe(mov,F);
     end
% save movie
    mov = close(mov);

Voila! (Make sure that you do not open any window over your plot window while MATLAB is compiling your movie, else those windows will become part of your movie)