Issue when running dyn.vf.Potential(adata, method = "umap") on data with precomputed umap coordinates.

[rohitarorayyc]

After running the following on an object with precomputed UMAP coordinates from Seurat:

adata = dyn.read('adata.h5ad') dyn.pp.recipe_monocle(adata) dyn.tl.dynamics(adata) dyn.tl.moments(adata) dyn.tl.reduceDimension(adata) dyn.tl.cell_velocities(adata) dyn.tl.cell_wise_confidence(adata) dyn.tl.gene_wise_confidence(adata, group='seurat_clusters', lineage_dict={0: [4]}) dyn.vf.VectorField(adata, basis='umap', M=100) dyn.vf.topography(adata, basis='umap') dyn.ext.ddhodge(adata, basis='umap')

I attempt to run "dyn.vf.Potential(adata, method = "umap") or dyn.vf.Potential(adata)" and end up with the error below in both cases:

---

KeyError Traceback (most recent call last) /var/folders/k3/0hvyvc1144lg85cq0yk0g5qr0000gn/T/ipykernel_31128/104691726.py in ----> 1 dyn.vf.Potential(adata, method = "umap")

~/.local/lib/python3.9/site-packages/dynamo/vectorfield/scPotential.py in Potential(adata, DiffMat, method, kwargs) 450 """ 451 --> 452 Function = adata.uns["VecFld"] 453 DiffMat = DiffusionMatrix if DiffMat is None else DiffMat 454 pot = Pot(Function, DiffMat, kwargs)

~/opt/anaconda3/lib/python3.9/site-packages/anndata/compat/_overloaded_dict.py in getitem(self, key) 98 return self.overloaded[key].get() 99 else: --> 100 return self.data[key] 101 102 def setitem(self, key, value):

KeyError: 'VecFld'

---

To try to remedy this issue, I ran the following lines of code:

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

and get this error:

---

TypeError Traceback (most recent call last) /var/folders/k3/0hvyvc1144lg85cq0yk0g5qr0000gn/T/ipykernel_31128/1199676603.py in ----> 1 dyn.vf.Potential(adata, method = "umap")

~/.local/lib/python3.9/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'

---

then, I tried to use

dyn.pp.recipe_monocle(adata) dyn.tl.dynamics(adata, cores=3)

dyn.tl.reduceDimension(adata) dyn.tl.cell_velocities(adata)

dyn.tl.cell_velocities(adata, basis='umap')

dyn.vf.VectorField(adata, basis='umap', M=100)

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

gene = "genename" dyn.pd.perturbation(adata, gene, [-100], emb_basis="umap", basis = "umap") dyn.pl.streamline_plot(adata, color=["core_edge_anno", gene], basis="umap_perturbation")

and get this error:

---

ValueError Traceback (most recent call last) /var/folders/k3/0hvyvc1144lg85cq0yk0g5qr0000gn/T/ipykernel_31128/2359643397.py in 1 gene = "CNFN" ----> 2 dyn.pd.perturbation(adata, gene, [-100], emb_basis="umap", basis = "umap") 3 dyn.pl.streamline_plot(adata, color=["core_edge_anno", gene], basis="umap_perturbation")

~/.local/lib/python3.9/site-packages/dynamo/prediction/perturbation.py in perturbation(adata, genes, expression, perturb_mode, cells, zero_perturb_genes_vel, pca_key, PCs_key, pca_mean_key, basis, emb_basis, jac_key, X_pca, delta_Y, projection_method, pertubation_method, J_jv_delta_t, delta_t, add_delta_Y_key, add_transition_key, add_velocity_key, add_embedding_key) 307 # calculate Jacobian 308 if jac_key not in adata.uns_keys(): --> 309 jacobian(adata, regulators=valid_genes, effectors=valid_genes) 310 311 Js = adata.uns[jac_key]["jacobian"] # pcs x pcs x cells

~/.local/lib/python3.9/site-packages/dynamo/vectorfield/vector_calculus.py in jacobian(adata, regulators, effectors, cell_idx, sampling, sample_ncells, basis, Qkey, vector_field_class, method, store_in_adata, **kwargs) 258 259 if vector_field_class is None: --> 260 vf_dict = get_vf_dict(adata, basis=basis) 261 if "method" not in vf_dict.keys(): 262 vf_dict["method"] = "sparsevfc"

~/.local/lib/python3.9/site-packages/dynamo/vectorfield/utils.py in get_vf_dict(adata, basis, vf_key) 231 232 if vf_key not in adata.uns.keys(): --> 233 raise ValueError( 234 f"Vector field function {vf_key} is not included in the adata object! " 235 f"Try firstly running dyn.vf.VectorField(adata, basis='{basis}')"

ValueError: Vector field function VecFld_pca is not included in the adata object! Try firstly running dyn.vf.VectorField(adata, basis='pca')

---

I was wondering how I could remedy this issue?

Thank you in advance!

[Xiaojieqiu]

Dear @Rohitarora21 thanks for using dynamo!

We recommend you to use dyn.ext.ddhodge(adata, basis='umap') instead of the other functions to calculate potential (or vector field based pseudotime).

Your second error is self-explanatory (did you read the error message?). You will need to run dyn.vf.VectorField(adata, basis='pca') first before you can use perturbation prediction. and you will also need to run dyn.tl.cell_velocities(adata, basis='pca') to predict RNA velocity to pca space before you can learn RNA velocity vector field in pca space.

[Mingsenli]

I meet the same problem. my code is :
adata = dyn.read('adata.h5ad') dyn.pp.recipe_monocle(adata) dyn.tl.dynamics(adata) dyn.tl.moments(adata) dyn.tl.gene_wise_confidence(adata, group='leiden_anno', lineage_dict={'E_cornea.basal': ['adult_cornea.superficial']}) dyn.tl.reduceDimension(adata) dyn.tl.cell_velocities(adata) dyn.tl.cell_velocities(adata, basis='pca') dyn.tl.cell_wise_confidence(adata) dyn.vf.VectorField(adata,basis='umap') dyn.vf.topography(adata, basis='umap') dyn.ext.ddhodge(adata, basis='umap') dyn.vf.Potential(adata) then an error occurs:

KeyError Traceback (most recent call last)

in ----> 1 dyn.vf.Potential(adata) ~/.local/lib/python3.8/site-packages/dynamo/vectorfield/scPotential.py in Potential(adata, DiffMat, method, **kwargs) 450 """ 451 --> 452 Function = adata.uns["VecFld"] 453 DiffMat = DiffusionMatrix if DiffMat is None else DiffMat 454 pot = Pot(Function, DiffMat, **kwargs) ~/.local/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py in __getitem__(self, key) 98 return self.overloaded[key].get() 99 else: --> 100 return self.data[key] 101 102 def __setitem__(self, key, value): KeyError: 'VecFld' Xiaojie gave the solution: "We recommend you to use dyn.ext.ddhodge(adata, basis='umap') instead of the other functions to calculate potential (or vector field based pseudotime)." I do run "dyn.ext.ddhodge(adata, basis='umap')". However, the error also occured. I really do not know how to solve this problem. Thank you

[Xiaojieqiu]

ddhodge can provide the same information of the potential and the Potential function is not currently well supported

[Mingsenli]

Hello, Dr. Qiu:

Dynamo is so excellent and  helps me a lot. Thank you very much for providing such a powerful tool.

When i run dyn.pd.perturbation, i am meeting an error. I really don’t know what caused this error. I sincerely hope you can help me solve this problem.

Thank you very much!

my code is :

dyn.pp.recipe_monocle(adata) dyn.tl.dynamics(adata, cores=48) dyn.tl.reduceDimension(adata)

dyn.tl.cell_velocities(adata,basis='pca') dyn.vf.VectorField(adata,basis='pca', M=1000) dyn.tl.cell_velocities(adata,basis='umap') dyn.vf.VectorField(adata,basis='umap', M=1000)            

dyn.vf.rank_velocity_genes(adata,                            groups='leiden_anno',                            vkey="velocity_S");

rank_speed = adata.uns['rank_velocity_S']; rank_abs_speed = adata.uns['rank_abs_velocity_S']; dyn.vf.acceleration(adata, basis='pca')

dyn.vf.rank_acceleration_genes(adata,                                groups='leiden_anno',                                akey="acceleration",                                prefix_store="rank"); rank_acceleration = adata.uns['rank_acceleration']; rank_abs_acceleration = adata.uns['rank_abs_acceleration'];

dyn.vf.curvature(adata, basis='pca');

dyn.vf.rank_curvature_genes(adata, groups='leiden_anno');

dyn.pp.top_pca_genes(adata, n_top_genes=500);   top_pca_genes = adata.var.index[adata.var.top_pca_genes];

top_pca_genes = ['RORA', 'PITX1','KRT3', 'KRT12',"MAL"] + list(top_pca_genes)

dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes);

dyn.ext.ddhodge(adata, basis='pca') dyn.ext.ddhodge(adata, basis='umap')

basis = "pca" dyn.vf.speed(adata, basis=basis) dyn.vf.divergence(adata, basis=basis) dyn.vf.acceleration(adata, basis=basis) dyn.vf.curvature(adata, basis=basis)

basis = "umap" dyn.vf.speed(adata, basis=basis) dyn.vf.divergence(adata, basis=basis) dyn.vf.acceleration(adata, basis=basis) dyn.vf.curvature(adata, basis=basis)

gene = "RORA" dyn.pd.perturbation(adata, gene, [-100], emb_basis="umap")

|-----> In silico perturbation of single-cells and prediction of cell fate after perturbation... |-----> Retrive X_pca, PCs, pca_mean... |-----> Calculate perturbation effect matrix via \delta Y = J \dot \delta X....

--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-25-d5be0df6f5b7> in <module> 1 gene = "RORA" ----> 2 dyn.pd.perturbation(adata, gene, [-100], emb_basis="umap") 3 #dyn.pl.streamline_plot(adata, color=["leiden_anno", gene], basis="umap_perturbation") ~/.local/lib/python3.8/site-packages/dynamo/prediction/perturbation.py in perturbation(adata, genes, expression, perturb_mode, cells, zero_perturb_genes_vel, pca_key, PCs_key, pca_mean_key, basis, emb_basis, jac_key, X_pca, delta_Y, projection_method, pertubation_method, J_jv_delta_t, delta_t, add_delta_Y_key, add_transition_key, add_velocity_key, add_embedding_key) 244 245 # project pca gene expression back to original gene expression: --> 246 X = pca_to_expr(X_pca, PCs, means) 247 248 # get gene position ~/.local/lib/python3.8/site-packages/dynamo/prediction/utils.py in pca_to_expr(X, PCs, mean, func) 489 # reverse project from PCA back to raw expression space 490 if PCs.shape[1] == X.shape[1]: --> 491 exprs = X @ PCs.T + mean 492 if func is not None: 493 exprs = func(exprs) TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'

    ------------------ Original ------------------ From: @.>; Date:  Fri, Apr 21, 2023 03:03 AM To: @.>; Cc: @.>; @.>; Subject:  Re: [aristoteleo/dynamo-release] Issue when running dyn.vf.Potential(adata, method = "umap") on data with precomputed umap coordinates. (Issue #353)

 

ddhodge can provide the same information of the potential and the Potential function is not currently well supported

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[Xiaojieqiu]

Dear @Mingsenli please create a new github issue for a separate question and format your code and error in a more readable format. I am delight to address your question after you doing that