If you are referring to the phase diagram as the 2-D phase plane plot, you can use a special output function called 'OutputFcn' and specify the function handle as '@odephas2' to plot it. By the way, there appear to be errors (extra \dot) in the LaTeX typesetting. The example below uses this system:
Please copy and paste the provided code into a script and save it as "mySystem.m" in the current working folder. To open the script, type "edit mySystem" in the Command Window, and to run it, simply enter "mySystem" in the Command Window.
options = odeset('OutputFcn', 'odephas2');
[t, x] = ode45(@odefcn, tspan, x0, options);
ax.XLabel.String = 'p(t)';
ax.YLabel.String = 'y(t)';
ax.Title.String = 'Phase Plane Plot';
function dx = odefcn(t, x)
dx(2,1) = - delta*gamma*beta*(y - yn) - delta*gamma*lambda*(p - pt);