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aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
https://dynamo-release.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Where is the [0,0] point of vector field? #384

Closed hyjforesight closed 1 year ago

hyjforesight commented 2 years ago

Hello Dynamo, When setting the initial cells and target cells for LAP, the fixed points which represent the cell state should be defined. I chose the fixed points 13, 6, 2, 5, 1, and found that the coordinates of these fixed points are negative.

good_fixed_points = [13, 6, 2, 5, 1] 
fixed_points=Xss[good_fixed_points]
fixed_points
array([[-5.91626328,  6.95178742],
       [-1.77828235,  0.4022991 ],
       [ 1.86099527, -1.50750829],
       [ 4.47594231,  9.27555429],
       [ 8.40929598,  4.43903784]])

I initially thought the left bottom point of the vector field should be the coordinate [0,0], but it wasn't. So I'm wondering where is the [0,0] point of the vector field. image

Thanks! Best, YJ

github-actions[bot] commented 1 year ago

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days

anshu957 commented 1 year ago

A little late to answer but might be useful for someone else: Basically, in dyn.pl.umap function you can supply additional arguments deaxis=False, despline=False to display umap co-ordinates.

Xiaojieqiu commented 1 year ago

Thank you for your answer @anshu957 ! I was busy with my job interviews before but I am now done with that. Please feel free to answer any additional questions.