Help with grouping of cells after integration

[hparaiso]

Hi, what is the best way to group cells by condition after integrating? I currently have two treatment groups which undergo standard QC processing (subset based on number of RNA reads and mitochondria levels) before I integrate them. After the integration process, I am having trouble deciphering which cells belong to the specific treatment group. I was using the object$groups function to group the cells, but I believe something is wrong with my grouping since there does not seem to be any difference in the cell numbers in the clusters. Thank you for the help!