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ValueError: Your adata doesn't have the key for Vector Field with None basis.

See original GitHub issue

Hi @Xiaojieqiu When running your zebrafish example, I encountered the following error when running dyn.pl.plot_energy(adata).

ValueError Traceback (most recent call last) ----> 1 dyn.pl.plot_energy(adata)

python3.8/site-packages/dynamo/plot/scVectorField.py in plot_energy(adata, basis, vecfld_dict, figsize, fig, save_show_or_return, save_kwargs) 1198 vf_key = "VecFld" if basis is None else "VecFld_" + basis 1199 if vf_key not in adata.uns.keys(): -> 1200 raise ValueError( f"Your adata doesn't have the key for Vector Field with {basis} basis." 1202 f"Try firstly running dyn.tl.VectorField(adata, basis={basis})."

ValueError: Your adata doesn't have the key for Vector Field with None basis. Try firstly running dyn.tl.VectorField(adata, basis=None).

Moreover, when changing the code to dyn.pl.plot_energy(adata, basis="umap"), I received the following error which seems due to the missing VecFld+basis key in our data.

KeyError Traceback (most recent call last)

----> 1 dyn.pl.plot_energy(adata, basis="umap")

python3.8/site-packages/dynamo/plot/scVectorField.py in plot_energy(adata, basis, vecfld_dict, figsize, fig, save_show_or_return, save_kwargs) 1205 vecfld_dict = adata.uns[vf_key] 1206 -> 1207 E = vecfld_dict["VecFld"]["E_traj"] if "E_traj" in vecfld_dict["VecFld"] else None 1208 tecr = vecfld_dict["VecFld"]["tecr_traj"] if "tecr_traj" in vecfld_dict["VecFld"] else None 1209

KeyError: 'VecFld'

Issue Analytics

State:
Created 2 years ago
Comments:5

Top GitHub Comments

1reaction

Xiaojieqiucommented, Oct 12, 2021

M is for the number control point and cannot be larger than the total cell number. Moreover, in general, it should only be a few hundred (like 100) because we only need a small number of control points to approximate the vector field which also gives tremendous computational speedup.

Please try python setup install the latest version of dynamo, pulled from this github repo. And then rerun the code I shared above. We will try to release a new version (1.0.1) on PyPi soon

0reactions

behroozazarkhalilicommented, Oct 12, 2021

M is for the number control point and cannot be larger than the total cell number. Moreover, in general, it should only be a few hundred (like 100) because we only need a small number of control points to approximate the vector field which also gives tremendous computational speedup.

Please try python setup install the latest version of dynamo, pulled from this github repo. And then rerun the code I shared above. We will try to release a new version (1.0.1) on PyPi soon

I will do so. I appreciate your clarification.

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