Comments on PR #111 + sharing trick we used for overlapping spots from overlapping capture areas

[lcolladotor]

Hi BayesSpace authors,

I saw PR https://github.com/edward130603/BayesSpace/pull/111 which seems interesting. I saw that you are changing some names, like row to array_row and stuff like that. I think that will be important to announce, as we'll have to update some of our code as users to match these changes.

Also, does the sanity check code at https://github.com/edward130603/BayesSpace/pull/111/commits/86de359d31ca7f25800bb8d5f570e95f8816a367#diff-2de0a6ab966efd85915ee3fa43a1f14c41edbde37cb62d758f551b8296b5febcR248-R260 affect the current joint clustering strategy listed at https://www.ezstatconsulting.com/BayesSpace/articles/joint_clustering.html#clustering-1? The one where you make an artificial array/row grid. It also doesn't seem to be the best practice (and if you ran BiocCheck you'd see this) to have a message() call with the word warning. If you consider this an actual warning, then I'd recommend using warning("some message", call. = FALSE).

Finally, I'd like to share with you a trick that @nick-eagles and I documented at https://research.libd.org/visiumStitched/articles/visiumStitched.html#defining-array-coordinates. Basically, we have cases where we can have overlapping data and assign 2 or more spots to the same array row/col hex grid locations, which then allows BayesSpace (and other tools using this hex grid info) to run spatial clustering using data from neighbors (and their overlapping spots). For more details, check also https://doi.org/10.1101/2024.08.08.607222.

Best, Leo