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theislab / cellrank

CellRank: dynamics from multi-view single-cell data
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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consider add more visualization tool for CellRank2 meets with experimental timepoint (waddington transport) #1221

Closed LiuCanidk closed 14 hours ago

LiuCanidk commented 1 week ago

... CellRank2 is great, but when I use the RealTimeKernel, I found very limited visualization functions for me to visualize my computing transition matrix. There were only RandomWalk and "single" flow.

I wonder if the development team could provide more APIs or functions to visualize the transition flow between clusters, at least not "single" flow one by one, but all cluster flows in one figure with color indicating IN/OUT direction and bandwidth indicating the flow mass size. Just like the figure below, which was published in 1. Marjanovic, N. D. et al. Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. Cancer Cell 38, 229-246.e13 (2020).

image

Or could you please give the user a tutorial on extracting the transition matrix and performing visualization analysis on our own?

Thanks in advance

Marius1311 commented 1 week ago

This is a great idea and we've been thinking about this for some time - unfortunately, we don't have the bandwith to implement this ourselves currently. Contributions from your side would be very welcome :)

WeilerP commented 14 hours ago

@LiuCanidk, every kernel has the attribute transition_matrix so you can easily use it to generate plots or perform a different analysis on it.

WeilerP commented 14 hours ago

I'll close this issue for now to keep the issues tractable.