Try this:
channel1 = sin(pi*[1:4096]/1024); % Create Data
channel2 = cos(pi*[1:4096]/1024); % Create Data
channel3 = sin(pi*[1:4096]/1024).*cos(pi*[1:4096]/2048); % Create Data
signal1 = channel1(1:4096);
signal2 = channel2(1:4096);
signal3 = channel3(1:4096);
figure(1);
% waterfall(signal1',signal2',signal3');
waterfall([signal1; signal2; signal3]); % Concatenate Vectors Into A Matrix