I am struggling to understand the trajectory. I read that black circles are nodes and the grey ones are their destinations, but I could not find the meaning of numbers in those circles.
I preprocessed adult mouse endothelial cells, aligned the 2 samples to remove the batch effect and then clustered the cells (exact protocol mentioned at Monocle3 website). I get three clusters denoting artery, vein and capillary endothelium.
When I split the cells into underlying samples (wt and ko), I see the same clusters. However, the cell arrangement in the clusters differs between the samples.
I do not see this when I cluster the cells using Seurat (after integration step). I am wondering whether Seurat performs over correction of the batch effect or Monocle3 underperforms the batch correction.
Kindly help me to understand these results.
