Hi,
I'm trying to use WOT on my own dataset. We have a time-course experiment from E12.5 et E18.5 (1 day separates each sample). But I don't really understand the time points that I am supposed to give for the computations.
In the notebook 3, for Composing couplings, your example is:
_gamma_8_10 = tmap_model.getcoupling(8, 10)
Does this command compute couplings between, 8-9-10, or 8-10 ...? Or, Do we have to compute this for any pairs of time point?
I did not find the function on Github to explore it.
Then, in Notebook 4, you write:
" In the following code block we generate probability vectors for the cell sets IPS, Neural, Trophoblast, and Stromal on day 18. The populations object is a list of these probability vectors for different cell."
Hi, I'm trying to use WOT on my own dataset. We have a time-course experiment from E12.5 et E18.5 (1 day separates each sample). But I don't really understand the time points that I am supposed to give for the computations.
In the notebook 3, for Composing couplings, your example is: _gamma_8_10 = tmap_model.getcoupling(8, 10) Does this command compute couplings between, 8-9-10, or 8-10 ...? Or, Do we have to compute this for any pairs of time point?
I did not find the function on Github to explore it.
Then, in Notebook 4, you write: " In the following code block we generate probability vectors for the cell sets IPS, Neural, Trophoblast, and Stromal on day 18. The populations object is a list of these probability vectors for different cell."
_tmap_model = wot.tmap.TransportMapModel.from_directory(TMAP_PATH) cell_sets = wot.io.read_sets(CELL_SETS_PATH, as_dict=True) populations = tmap_model.population_from_cell_sets(cell_sets, at_time=12)_
So, how did you select the time 12? And, Do we need to compute this for all the time points?
Actually, I do not understand how to choose the time points to run the analysis... If you can explain to me a bit more about your choices. Best,