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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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[Dimensionality reduction] method: ForceAtlas2 #266

Closed andrew-benz closed 1 month ago

andrew-benz commented 3 years ago

What is the method? ForceAtlas2 is a force-directed graph layout algorithm. Although it was originally designed for visualizing networks, ForceAtlas2 and other force-directed layout algorithms have become popular for visualizing single-cell datasets. This paper by Jacomy et. al. describes the algorithm in more depth.

Where is the code located? https://github.com/bhargavchippada/forceatlas2

Which task(s) could it be used for? Dimensionality reduction

dkobak commented 3 years ago

https://github.com/singlecellopenproblems/SingleCellOpenProblems/issues/264

LuckyMD commented 3 years ago

Is this different from scanpy.tl.draw_graph? I believe there's an fa2 version for that. Although I think there might be faster libs out there. But this would be easy to implement.

dkobak commented 3 years ago

It's the same:

The default layout (‘fa’, ForceAtlas2) [Jacomy14] uses the package fa2 [Chippada18], which can be installed via pip install fa2.

https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.draw_graph.html

github-actions[bot] commented 1 month ago

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