so for some reasons if a node doesn’t have any parents it will be positioned to deeper level, some of my nodes are positioned at right most because they don’t have any links
If that doesn’t do it, you could override LayeredDigraphLayout | GoJS API to call the super method and then adjust the layers of all of the vertexes to suit your needs.
Can you show us your code so we can reproduce this? Also, please enter real information in your profile for your company if you’d like continued support.