Aggregate cells by metadata category and plot against another category

[ShanSabri]

Is it possible to aggregate cells by a specific metadata category, say Donor, and compare across another metadata category like Treatment status? I find this way to be easier to interpret for data with many (>200k) cells. If I were to do this comparison at the cell level with a gene that is highly dropped out or lowly expressed then the distribution would be heavily weighted towards zero but if I were to aggregate by mean or median then the data looks a bit cleaner and easier to interpret.

[z5ouyang]

Thanks for the suggestion. To make sure I understand it correctly: instead of using each individual cells, you propose to obtain pseudo bulk samples by a category such as Donor? And now each dot is a pseudo bulk rather than a cell in any plots? or a specific plot you are thinking of?

[ShanSabri]

Yep, exactly