Simulating both spatial and condition effect

[AlanTeoYueYang]

Dear team, Thank you so much for the package, it is really useful. However, I am curious if you can simulate both spatial and condition effects using sc3design? I have a comparative spatial experiment and I want to be able to simulate both spatial and condition effect. Furthermore, I wonder if we can alter the condition effect in said simulation as shown in https://songdongyuan1994.github.io/scDesign3/docs/articles/scDesign3-conditionEffect-vignette.html? From what I gathered in the tutorials, the spatial simulation uses a different mu formula s(x, y, bs = 'gp', k= 400) than the condition effect cell_type + condition + cell_type*condition". How should I combine them?

[SONGDONGYUAN1994]

Hi Alan,

This is a really good question. One intuitive idea is to set s(x, y, bs = 'gp', k= 400, by = condition) so that each condition will have a different spatial surface. However, you need to make sure that the spatial coordinates from multiple samples have been aligned.

I wonder if you would like to set up a meeting to further discuss this problem. Email me (dongyuansong@ucla.edu) if you would like to do so.

Best regards, Dongyuan