Closed eynullazada closed 3 years ago
Never mind. I solved the issue
@eynullazada, sorry for the late reply. Was the issue related to scVelo? If not, I believe we can close the issue?
I also ran into this error, @eynullazada how did you solve this issue?
I also ran into this error, @eynullazada how did you solve this issue?
Hi
I found out actually scvelo filters out many genes while calculating velocity and maker genes that I was interested in were filtered out too. I confirmed it by visualizing random genes that are not filtered.
I hope it helps
Khagani
It works perfectly fine! Thank you!
when I execute the command : scv.pl.velocity(adata, ['Cpe', 'Gnao1', 'Ins2', 'Adk'], ncols=2)
it gives the following error: _>>> scv.pl.velocity(adata, ['Cpe', 'Gnao1', 'Ins2', 'Adk'], ncols=2,save='pancreas_genes2') Traceback (most recent call last): File "", line 1, in
File "/mnt/ws/home/keynullazada/.conda/envs/p3_env/lib/python3.8/site-packages/scvelo/plotting/velocity.py", line 152, in velocity
gs = pl.GridSpec(nrows, ncols, wspace=0.5, hspace=0.8)
File "/mnt/ws/home/keynullazada/.conda/envs/p3_env/lib/python3.8/site-packages/matplotlib/gridspec.py", line 420, in init
GridSpecBase.init(self, nrows, ncols,
File "/mnt/ws/home/keynullazada/.conda/envs/p3env/lib/python3.8/site-packages/matplotlib/gridspec.py", line 48, in init
raise ValueError(
ValueError: Number of rows must be a positive integer, not 0
my data: _>>> adata AnnData object with n_obs × n_vars = 37001 × 2000 obs: 'initial_size_spliced', 'initial_size_unspliced', 'initial_size', 'n_counts', 'velocity_self_transition', 'louvain' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand', 'gene_count_corr', 'means', 'dispersions', 'dispersions_norm', 'highly_variable', 'velocity_gamma', 'velocity_r2', 'velocity_genes' uns: 'pca', 'neighbors', 'velocity_params', 'velocity_graph', 'velocity_graph_neg', 'umap', 'louvain', 'louvain_colors' obsm: 'X_pca', 'X_umap', 'velocity_umap' varm: 'PCs' layers: 'ambiguous', 'matrix', 'spliced', 'unspliced', 'Ms', 'Mu', 'velocity', 'variancevelocity' obsp: 'distances', 'connectivities'
Error
```pytb ... ```Versions:
looking forward to hearing from you
Khagani