You'll need to subtract the XY centre of your image from the points before you measure the angle using atan2. The following code might help clear things up a bit:
%this is the center of the image
image_center_xy = [.5 .5];
%here are some random points:
x = rand(10,1); y = rand(10,1);
%plot the points:
scatter(x,y);hold on
axis([0 1 0 1])
%pick a point with the mouse
[X,Y] = ginput(1);
%find the distances between click and the data:
distances = sqrt((x-X).^2 + (y-Y).^2);
%find the closest point to to the mouse click:
point0idx = find(distances == min(distances));
%replot the chosen point as a filled circle:
scatter(x(point0idx),y(point0idx),'filled');
%compute angles:
angles = -atan2(y-image_center_xy(2),x-image_center_xy(1));
%make the chosen point an angle of zero (and use modulo for folded angles):
angles = mod(angles - angles(point0idx),2*pi);
%sort by angle:
[angles, idx] = sort(angles);
%sort everything by the angle index:
x = x(idx); y = y(idx);
%plot the line of the ordered points:
plot(x,y,'r'); hold off
Did I understand your question correctly?
