agglomerateByRanks defaults to assay silently – consider requiring assay.type or messaging

[0xMuluh]

agglomerateByRanks() silently uses the default assay (apparently counts) and only a warning about negative values hinted at the chosen assay. When objects have multiple assays, this can easily cause mistakes if users expect relabundance or other assay.

consider?

• requiring explicit assay.type when multiple assays exist (error with message), and/or
• emitting a message like “Using assay: counts” when assay.type is omitted