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add trajectory lines to dim. plots #16

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Zaf4 opened this issue Feb 10, 2025 · 4 comments
Open

add trajectory lines to dim. plots #16

Zaf4 opened this issue Feb 10, 2025 · 4 comments
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enhancement New feature or request

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@Zaf4
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Zaf4 commented Feb 10, 2025

Such as the image below trajectories denoted by arrows.

Can be implemented in letsplot using.
geom_curve()

https://lets-plot.org/python/pages/api/lets_plot.geom_curve.html

Image

@Zaf4 Zaf4 added the enhancement New feature or request label Feb 14, 2025
@Zaf4
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Zaf4 commented Feb 14, 2025

related reading: https://joynyaanga.com/post/ti/

@Zaf4
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Zaf4 commented Feb 14, 2025

Velocity embedding calculation witihin

scv.pl.velocity_embedding_stream()

https://github.com/theislab/scvelo/blob/main/scvelo/plotting/velocity_embedding_stream.py#L128

@Zaf4
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Zaf4 commented Feb 14, 2025

scv.tools.velocity_embedding(adata, basis="umap")

this is an in-place operation that adds f"velocity_{basis}" key to obsm.
"velocity_umap" in this case (umap is also the default value

adata.obsm.["velocity_*"]
is a np.ndarray with dimensions of n_obs * 2.

@Zaf4
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Zaf4 commented Feb 19, 2025

https://github.com/matplotlib/matplotlib/blob/v3.10.0/lib/matplotlib/streamplot.py

matplotlib has a stream plot that is not present in letsplot (closest is geom_curve)

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