Plotting Pseudotime Values

[anemartinezlarrinaga2898]

Hello I have been several weeks to try to understand the library and how the analysis work!

Im on the point of plotting the pseudo time values in my UMAP however it seems the values of the pseudo time are inverted and it seems to happen the same in the tutorial from the fibrosis dataset (https://hectorrdb.github.io/condimentsPaper/articles/Fibrosis.html)

The attached picture is from the tutorial. The starting point is marked where the yellow color is the AT1 cluster.. so there is something im not following because as far as I understood if the AT1 are the starting point should not be marked as 0?

This is what Im getting and the starting point is where the yellow color is.

Best,
ANE

[HectorRDB]

HI,
The fibrosis dataset is a peculiar example of lineages converging to a common end point, hence the pseudotimes values. You will need to remove the line pst = max(pst) - pst) in your code to have a "normal" pseudotime behavior.