TypeError: fit() missing 3 required positional arguments: 'adata', 'x_lim', and 'y_lim'

I encountered the following error when calling dyn.vf.Potential(adata)

import dynamo as dyn
dyn.get_all_dependencies_version()
adata = dyn.sample_data.DentateGyrus()

dyn.pp.recipe_monocle(adata)
dyn.tl.dynamics(adata)

dyn.tl.reduceDimension(adata, basis='umap', enforce=True)
dyn.tl.cell_velocities(adata, basis='umap')
dyn.tl.cell_wise_confidence(adata)

dyn.vf.VectorField(adata, basis='umap')
dyn.vf.topography(adata, basis='umap')

dyn.ext.ddhodge(adata, basis="umap")

adata.uns["VecFld"] = adata.uns.get("VecFld_umap")
dyn.vf.Potential(adata)

---

TypeError Traceback (most recent call last) ----> 1 dyn.vf.Potential(adata)

python3.8/site-packages/dynamo/vectorfield/scPotential.py in Potential(adata, DiffMat, method, **kwargs) 453 DiffMat = DiffusionMatrix if DiffMat is None else DiffMat 454 pot = Pot(Function, DiffMat, **kwargs) –> 455 pot.fit(method=method) 456 457 return adata

TypeError: fit() missing 3 required positional arguments: 'adata', 'x_lim', and 'y_lim'

[Xiaojieqiu]

certainly, will do! we are delayed in updating those because of other commitments recently but will start to work on updating dynamo and all related readthedocs pages largely starting from next week. Thanks!

[behroozazarkhalili]

I see the issue now, looks like you are following the 10 minutes to dynamo section (unfortunately both the Potential function and that section have not been updated because of historical reasons— can fix those next week). I would suggest you start with other tutorials, such as zebrafish, to get started with dynamo:

https://dynamo-release.readthedocs.io/en/latest/notebooks/zebrafish.html

Please also update the last cell of the tutorial as well since it also raises an error.

import matplotlib.pyplot as plt

fig1, f1_axes = plt.subplots(ncols=2, nrows=2, constrained_layout=True, figsize=(12, 10))
f1_axes
f1_axes[0, 0] = dyn.pl.cell_wise_vectors(adata, color='umap_ddhodge_potential', pointsize=0.1, alpha = 0.7, ax=f1_axes[0, 0], quiver_length=6, quiver_size=6, save_show_or_return='return')
f1_axes[0, 1] = dyn.pl.grid_vectors(adata, color='speed_umap', ax=f1_axes[0, 1], quiver_length=12, quiver_size=12, save_show_or_return='return')
f1_axes[1, 0] = dyn.pl.streamline_plot(adata, color='divergence_pca', ax=f1_axes[1, 0], save_show_or_return='return')
f1_axes[1, 1] = dyn.pl.topography(adata, color='acceleration_umap', ax=f1_axes[1, 1], save_show_or_return='return')
plt.show()