A = [1 0 0 1 1 1
0 2 0 2 0 2
0 0 3 0 3 3];
To sort only the positive values, the zero values are set to NaN:
A(A==0) = nan;
Now sort each column:
for i=1:size(A,2), A(:,i) = sort(A(:,i)); end
Replace the NaN with zeros:
A(isnan(A)) = 0;
Add a new final row of zeros:
A(end+1, end) = 0;
Set all zeros to the maximum element in A + 1:
A(A==0) = max(A(:)) + 1;
