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Waddington-OT #89
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Given that the time prior information is now included in dynwrap, this should be easy to wrap |
I've looked into adding Waddington-OT (See exploratory script). With some example data, I've managed to run However, from the tmaps_* files, I'm not sure how I would convert this into our format; something like this:
Perhaps @robindar or @joshua-gould could chime in on how we could convert one format into the other? Could I use the tmaps_* files, calculate an MST, and use this as my milestone_network? |
You want to convert the transport maps to long format, correct?
…On Tue, Jul 31, 2018 at 5:22 AM, Robrecht Cannoodt ***@***.*** > wrote:
I've looked into adding Waddington-OT (See exploratory script
<https://github.com/dynverse/dynmethods/blob/feature/add_wot/containers/wot/run.py>).
With some example data, I've managed to run wot optimal_transport, wot
force_layout, and wot trajectory (See example_data.zip
<https://github.com/dynverse/dynmethods/files/2244594/example_data.zip>
for input and output files).
However, from the tmaps_* files, I'm not sure how I would convert this
into our format; something like this:
> data$milestone_network
# A tibble: 3 x 4
from to length directed
<chr> <chr> <dbl> <lgl>
1 M3 M4 0.619 TRUE
2 M1 M3 0.876 TRUE
3 M3 M2 0.442 TRUE
> data$progressions
# A tibble: 300 x 4
cell_id from to percentage
<chr> <chr> <chr> <dbl>
1 C1 M3 M2 0.206
2 C2 M3 M4 0
3 C3 M1 M3 0.966
4 C4 M3 M4 0.690
5 C5 M1 M3 1
6 C6 M1 M3 0.321
7 C7 M3 M2 0.129
Perhaps @robindar <https://github.com/robindar> or @joshua-gould
<https://github.com/joshua-gould> could chime in on how we could convert
one format into the other? Could I use the tmaps_* files, calculate an MST,
and use this as my milestone_network?
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Hello Joshua! No, not exactly. We want to convert the transport maps to our 'common trajectory format' (See Figure 1 in our bioRxiv). Converting the transport maps to a long format would result in a graph that is way too dense. In order to make it less sparse, I could calculate an MST, but I'm not sure this is the spirit of wot. Robrecht |
Hello Robrecht, From what I understand, all methods compared in this paper are trying to build a graph (with different constraints) that best describes the evolution of the cells, and then project all cells to its edges, to get the progression values of your example. David |
Thanks for this information, David :) Based on your explanation, we will exclude Waddington-OT from the benchmark for now. Kind regards, |
https://pypi.org/project/wot/
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