How about the following?
% First point position in the matrix
M1 = [0 0 0 1 0 0 0;
0 0 0 0 0 0 0;
0 0 0 0 0 0 0;
0 0 0 0 0 0 0];
% Next time period the matrix will have other values for the second "blue" point
M2 = [0 0 0 0 0 0 0;
0 0 0 0 0 0 0;
0 0 0 0 0 0 0;
0 0 0 0 0 1 0];
[row,col] = find(M1 | M2);
row2 = (1:4)';
col2 = round(interp1(row,col,row2));
M3 = zeros(size(M1));
M3(sub2ind(size(M3),row2,col2)) = 1;
The result is:
>> M3
M3 =
0 0 0 1 0 0 0
0 0 0 0 1 0 0
0 0 0 0 1 0 0
0 0 0 0 0 1 0
