Branching points detection

[pwl]

Is there any way to estimate the number of branching points? It seems that this number has to be explicitly given before running the algorithm, which might be difficult if it's not clear from simply looking at the dimensionally reduced data.

[falexwolf]

No, there is no such way in DPT. We had good experience with manually choosing it. In our opinion, no one really came up with a sound and reliable statistical way of detecting the number of branching points, independent of the underlying algorithm. The best attempts to solve the problem though might be found within Monocle 2 or K-Branches.

[ShuhuaGao]

Yes, it seems better to specify the number of branches manually. I have tried Monocle 2 though, which gives about 10 branches for the example dataset from Moignard et al., Nat. Biotechn. (2015). Maybe I didn't operate Monocle 2 properly.

[falexwolf]

Thanks for the feedback! It astonishes me a bit, though, that Monocle 2 doesn't work well on that example. For the Paul et al, Cell (2015), it should give very nice results (link to preprocessing / link to plots), as they show in the recent preprint I reference above.

[falexwolf]

The approx. graph abstraction (AGA) tool resolves this issue: https://doi.org/10.1101/208819 and https://github.com/theislab/graph_abstraction.