Does dec_cci_all() exclude same-cell-type interactions? How to include autocrine pairs?

[Zijiang8]

Dear Spatalk Developers,

Thank you for this powerful tool—it has significantly enhanced our spatial cell-cell interaction analysis. During my analysis using dec_cci_all(), I noticed the output states: > obj_default <- dec_cci_all(obj_default) Note: there are 7 cell types and 42 pair-wise cell pairs

With 7 cell types, I expected 7×7=49 possible pairs (including same-type interactions like AT1—AT1). However, only 42 pairs (7×6) were computed. Does dec_cci_all() intentionally exclude same-cell-type interactions? And results only include interactions between different cell types (e.g., AT1—AT2). Is there a way to include autocrine interactions (same-type pairs) in the analysis?

Could you suggest a solution? Understanding this is crucial for our study on self-signaling mechanisms.

Thank you for your time and brilliant work!

Best regards, Zijiang

[Xieyuanfen]

Hello, Zijiang8 , when I ran the function "find_lr_path", the code reported an error: The error occurred in base::rowSums(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array, and it must have at least two dimensions. Could you please explain how you managed to successfully complete this step?