1.) Actually, you do not need to specify size and color. If you only provide three properties (X,Y,Z spatial positions) it will assume that all spheres have the same diameter and color, so it will append these as value 1.

if size(coord,2) == 3
fprintf('Assuming all spheres are of same size and color\n');
coord = [coord, ones(size(coord,1),2)];
end

2.)  The node size is specified in mm, but you can scale this in the GUI using the "Scale" slider or using the NODESIZE() script command. The colors are an intensity that are relative to each other, so if you have colors 1,2,3 and chose the Red-yellow color scheme with a threshold of 1..3 then the colors would be red,orange and yellow, where if you set the threshold to 0..1 they would all be yellow. Likewise, you could chose a different color scheme. The easiest way to understand this it to run my script and then adjust the threshold, color and size widgets in the "Nodes" panel (see attached screenshot)