I'm currently following the WOT tutorials, in particular, the trajectory visualisation part in Notebook 4. I plotted the probabilities for a cell type trajectory in a different dataset and noticed that cells with high trajectory probabilities do not necessarily reside in similar UMAP positions (see below). I was wondering how this can be the case? I understand that the probabilities inferred through optimal transport are in part, influenced by Euclidean distances, so perhaps naively, I was expecting the trajectory to move relatively smoothly across the UMAP. I computed mean Euclidean distances with the cell type of interest (circled below) and the cluster highlighted on the right has a much larger value than the neighbouring cell types on the left-hand side. What might be causing the cells on the right to be marked as ancestors in this case?
Hi,
I'm currently following the WOT tutorials, in particular, the trajectory visualisation part in Notebook 4. I plotted the probabilities for a cell type trajectory in a different dataset and noticed that cells with high trajectory probabilities do not necessarily reside in similar UMAP positions (see below). I was wondering how this can be the case? I understand that the probabilities inferred through optimal transport are in part, influenced by Euclidean distances, so perhaps naively, I was expecting the trajectory to move relatively smoothly across the UMAP. I computed mean Euclidean distances with the cell type of interest (circled below) and the cluster highlighted on the right has a much larger value than the neighbouring cell types on the left-hand side. What might be causing the cells on the right to be marked as ancestors in this case?
Many thanks,
Dan