So, If I understood correctly, you want to plot the average of connectivity spectrum (Frequency by time) among all pairs of a N x N matrix?
Paul, first of all, you need to use a measure which produces that 4-D structure (channels x channels x time x frequency band). Right now, you can use time-resolved coherence. You can specify the time window and frequency resolution. Make sure to select overlap as large as possible so you would have a better temporal resolution.
When you computed the connectivity matrix, you can export it to Matlab. The output variable will be a structure. There is a field inside the structure named as TF with the following dimensions:
(N^2+N)/2 x time points x frequency bins
It is lower-triangle of the original connectivity matrix. Average on the first dimension (Exclude the diagonal elements). Finally, use "imagesc" to display the connectivity spectrum.
Hossein