Sorry this is not an issue, rather my problem; URD requires user to define some cluster of cells (tips) at the last time point.
What URD gave me by 3 time points is this picture
ibb.co/cWorp9
[blue](url
)
Blue is last time point that has three tips (A, B, C) ,green is between time point and red is root cells (first time point).
In my system (amoeba) I know cells in the earliest time point can be grouped to at least 3 groups of cells (by Seurat R), while here by URD I just have a mass of cells in earliest time point (may be this is true in vertebrate system where we have pluripotent cells). How I can use my clusters of cells at the earliest time point to plot such a tree please?
Sorry this is not an issue, rather my problem; URD requires user to define some cluster of cells (tips) at the last time point. What URD gave me by 3 time points is this picture
ibb.co/cWorp9
[blue](url
Blue is last time point that has three tips (A, B, C) ,green is between time point and red is root cells (first time point). In my system (amoeba) I know cells in the earliest time point can be grouped to at least 3 groups of cells (by Seurat R), while here by URD I just have a mass of cells in earliest time point (may be this is true in vertebrate system where we have pluripotent cells). How I can use my clusters of cells at the earliest time point to plot such a tree please?
Thanks a lot