3d graph layout drawing (gephi/Matlab)

I have tried to drawn image in matlab like the below
https://i.stack.imgur.com/kRDAf.jpg
But I want to draw like in the below figure
https://i.stack.imgur.com/GcY2m.jpg
Can anyone please help me or suggest some way to do it in gephi or matlab or any other ways?

Thank you so much!