How to change the FFT phase domain of each frame by 90 degrees
It sounds like you're trying to plot the FFT such that the result is centered at 0, instead of at Fs. Matlab has a function for this fftshift.

Here's a simple example when trying to plot either the onesided or twosided FFT.

f = 100; % Signal frequency (Hz)
fs = 1024; % Sampling frequency (Hz)
N = 1024; % Number of samples
Nfft = 1024; % FFT size

xf = 20*log10(abs(fft(x, Nfft))); % Compute the PSD

fw1 = fs * (0:Nfft/2)./Nfft; % Onesided domain
fw2 = fs * (-Nfft/2:Nfft/2-1)./Nfft; % Twosided domain

figure
subplot(211), plot(fw1, xf(1:Nfft/2+1)), title('Onesided')
subplot(212), plot(fw2, fftshift(xf)), title('Twosided')