Correlation of cells between datasets with different kinetics

[No2Ross]

Hi.

I've been trying to test out a trajectory alignment method using dyngen datasets with different kinetics and i wanted to look at the correlation of the cells from the two datasets across a pseudotime axis and i noticed they are basically completely uncorrelated (spearmans ~ 0) across the process.

I wondered if i was just doing something wrong, so i simulated two new datasets which have the same generate_kinetics() in the model but generate_cells() and generate_gold_standard() are ran independently and these two correlate well across the common path.

In your paper the trajectory alignment figure (below) seems to indicate that the two share a common process but the disease moves quicker through the process so you'd assume that some parts would be correlated between the trajectories, but there would just be a time offset between them, but this does not seem to be the case.

I'm thus wondering if there's something i'm missing when simulating the dataset, or if there are some parameters i can change in order to achieve this?

Thanks, Ross