DSTG link graph add connections between real spots?

[RemyLau]

According to the link graph construction description from the paper, the graph should also contain interaction between real-spots.

However, in the current implementation (modified from the original implementation, see https://github.com/Su-informatics-lab/DSTG/issues/16), only the cross interactions between pseudo-spots and real-spots are used.

https://github.com/OmicsML/dance/blob/9966c47ed2b3e76af2b10db7a170caf6ced59fb8/dance/transforms/graph/dstg_graph.py#L59

Should we add the interactions between real-spots as described in the manuscript in the DANCE implementation? If so, it could be achieved quite easily by simply calling construct_link_graph one more time by passing real_st_df as both first two args and combine the edge list with the old graph.

Caution: be aware that one might need to modify the the new graph node indexes (or pass real_st_df and another copy of real_st_df with offsetted index)

[RemyLau]

The authors have confirmed that we should combine both graphs (see https://github.com/Su-informatics-lab/DSTG/issues/16#issuecomment-1370179417).