Hi cricketking13,
if you don't want to have lsim plot the default plot, just "collect" the output and plot as you desire:
%% LPF
order = 3;
ripple = 1; %pass band ripple
f_c = 22e6;
[num1, den1] = cheby1(order, ripple, 2*pi*1.10*f_c, 'low', 's');
%% Create input signal
Fs = 200e6;
Ts = 1/Fs;
NFFT = 2^12;
Runtime = (NFFT-1)*Ts;
t = 0:Ts:Runtime;
a_in = 1;
fin = 5e6;
phase_in = 0;
y_in = a_in * sin( 2 * pi * fin * t + phase_in ); % 4096 points
%% filter signal
% create system
myFilter = tf(num1,den1);
% apply filter to time domain signal
[y_out, time] = lsim(myFilter,y_in,t);
% plot without y_in
plot(time,y_out')
Kind regards,
Robert
