I am trying to graph this scatter plot on a 3D scatter plot using the packages plot3D and plot3Drgl. However, I am having trouble doing so. What would be the best way to accomplish this. Thanks, I'm very new to R.

I've tried using scatterplot3d, but I want to be able to rotate it. Also, I want there to be no depth on the 3D plot, and specifically, I have to use those packages in order to make the plot.

I don't know how to upload an interactive plot here. If you run this, you'll get a new window where you will be able to rotate, zoom, etc. You can explore more options from the documentation.

Note that, I only plotted the points, instead of joining them. I didn't quite understand how did you plot your diagram. One of the points (labelled Sada-Melik or something like that) is connected to two points, which makes me think that you may be plotting vertices and edges separately. If you want to plot a graph, I think igraph package will be useful, but I haven't used it much.