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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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Unable to import scvelo #1216

Closed jjia1 closed 4 months ago

jjia1 commented 4 months ago

Hello, Thanks for developing scvelo.

Just some background, I wanted to perform RNA velocity analysis on my object but I had been working in Seurat initially. I performed some data conversion from Seurat into Scanpy using sceasy or some other packages.

I was trying to get the tool running, but I'm unable to import the package when using the newest version if i use the command: pip install git+https://github.com/theislab/scvelo

This is the output from import scvelo as scv with version 0.3.1

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[2], [line 2](vscode-notebook-cell:?execution_count=2&line=2)
      [1](vscode-notebook-cell:?execution_count=2&line=1) # if any installation issues, remember to use lower version of scvelo (like 0.2.4)
----> [2](vscode-notebook-cell:?execution_count=2&line=2) import scvelo as scv

File [~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:6](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:6)
      [3](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:3) from scanpy import read, read_loom
      [5](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:5) from scvelo import datasets, logging
----> [6](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:6) from scvelo import plotting as pl
      [7](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:7) from scvelo import preprocessing as pp
      [8](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/__init__.py:8) from scvelo import settings

File [~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:3](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:3)
      [1](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:1) from scanpy.plotting import paga_compare, rank_genes_groups
----> [3](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:3) from .gridspec import gridspec
      [4](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:4) from .heatmap import heatmap
      [5](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/__init__.py:5) from .paga import paga

File [~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:6](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:6)
      [3](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:3) import matplotlib.pyplot as pl
      [5](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:5) # todo: auto-complete and docs wrapper
----> [6](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:6) from .scatter import scatter
      [7](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:7) from .utils import get_figure_params, hist
      [8](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.8/site-packages/scvelo/plotting/gridspec.py:8) from .velocity_embedding import velocity_embedding
...
     [69](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/.local/lib/python3.8/site-packages/optax/contrib/dadapt_adamw.py:69)     A `GradientTransformation` object.
     [70](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/.local/lib/python3.8/site-packages/optax/contrib/dadapt_adamw.py:70)   """
     [72](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/.local/lib/python3.8/site-packages/optax/contrib/dadapt_adamw.py:72)   def init_fn(params: base.Params) -> DAdaptAdamWState:

TypeError: 'type' object is not subscriptable
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?a835cbc0-31ed-47ae-95c1-330852a6d7e4) or open in a [text editor](command:workbench.action.openLargeOutput?a835cbc0-31ed-47ae-95c1-330852a6d7e4). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

However if I downgrade to an older version, specifically 0.2.4, with pip install scvelo==0.2.4.0 I'm able to import the package but I get errors down the line when trying to run the package. Doesn't matter what command I use, I get the following error. As seen when i use scv.pl.proportions(velo)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[15], [line 1](vscode-notebook-cell:?execution_count=15&line=1)
----> [1](vscode-notebook-cell:?execution_count=15&line=1) scv.pl.proportions(velo, layers = ['spliced', 'unspliced'])

File [~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62), in proportions(adata, groupby, layers, highlight, add_labels_pie, add_labels_bar, fontsize, figsize, dpi, use_raw, show, save)
     [60](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:60)     layers = ["spliced", "unspliced", "ambigious"]
     [61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:61) layers_keys = [key for key in layers if key in adata.layers.keys()]
---> [62](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62) counts_layers = [sum(adata.layers[key], axis=1) for key in layers_keys]
     [64](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:64) if use_raw:
     [65](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:65)     ikey, obs = "initial_size_", adata.obs

File [~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62), in <listcomp>(.0)
     [60](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:60)     layers = ["spliced", "unspliced", "ambigious"]
     [61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:61) layers_keys = [key for key in layers if key in adata.layers.keys()]
---> [62](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:62) counts_layers = [sum(adata.layers[key], axis=1) for key in layers_keys]
     [64](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:64) if use_raw:
     [65](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/plotting/proportions.py:65)     ikey, obs = "initial_size_", adata.obs

File [~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:124](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:124), in sum(a, axis)
    [107](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:107) def sum(a: Union[ndarray, spmatrix], axis: Optional[int] = None) -> ndarray:
    [108](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:108)     """Sum array elements over a given axis.
    [109](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:109) 
    [110](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:110)     Arguments
   (...)
...
--> [124](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:124)     if a.ndim == 1:
    [125](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:125)         axis = 0
    [127](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/rnavelo/lib/python3.8/site-packages/scvelo/core/_arithmetic.py:127)     with warnings.catch_warnings():

AttributeError: 'AnnData' object has no attribute 'ndim'
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?108bb7d5-d72b-4eb0-9f16-3e0a647f73d3) or open in a [text editor](command:workbench.action.openLargeOutput?108bb7d5-d72b-4eb0-9f16-3e0a647f73d3). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

This is what my data looks like as an AnnData object

AnnData object with n_obs × n_vars = 74037 × 20881
    obs: 'nCount_RNA', 'nFeature_RNA', 'orig.ident', 'mitochondrial_fraction', 'ribosomal_fraction', 'label', 'nCount_SCT', 'nFeature_SCT', 'seurat_clusters', 'cell_lineage', 'SCT_snn_res.0.6', 'celltype', 'celltype_highres', 'experiment', 'condition', 'timepoint', 'condition_timepoint', 'cell_group', 'gene_name', 'nCount_unspliced', 'nFeature_unspliced'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'celltype', 'celltype_colors', 'celltype_highres_colors', 'celltypehighres_colors', 'condition_colors', 'condition_timepoint_colors', 'experiment_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'seurat_clusters_colors', 'timepoint_colors', 'tsne', 'umap'
    obsm: 'X_pca', 'X_tsne', 'X_umap', 'X_umap2'
    varm: 'PCs'
    layers: 'spliced', 'unspliced'
    obsp: 'connectivities', 'distances'
jjia1 commented 4 months ago

I solved the import issue. If I upgraded to Python 3.9, the dependency issue was resolved but I still run into the ndim issue with my dataset.

velo

AnnData object with n_obs × n_vars = 74037 × 20881
    obs: 'nCount_RNA', 'nFeature_RNA', 'orig.ident', 'mitochondrial_fraction', 'ribosomal_fraction', 'label', 'nCount_SCT', 'nFeature_SCT', 'seurat_clusters', 'cell_lineage', 'SCT_snn_res.0.6', 'celltype', 'celltype_highres', 'experiment', 'condition', 'timepoint', 'condition_timepoint', 'cell_group', 'gene_name', 'nCount_unspliced', 'nFeature_unspliced'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'celltype', 'celltype_colors', 'celltype_highres_colors', 'celltypehighres_colors', 'condition_colors', 'condition_timepoint_colors', 'experiment_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'seurat_clusters_colors', 'timepoint_colors', 'tsne', 'umap'
    obsm: 'X_pca', 'X_tsne', 'X_umap', 'X_umap2'
    varm: 'PCs'
    layers: 'spliced', 'unspliced'
    obsp: 'connectivities', 'distances'

scv.pl.proportions(velo)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[13], [line 1](vscode-notebook-cell:?execution_count=13&line=1)
----> [1](vscode-notebook-cell:?execution_count=13&line=1) scv.pl.proportions(velo)

File [~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61), in proportions(adata, groupby, layers, highlight, add_labels_pie, add_labels_bar, fontsize, figsize, dpi, use_raw, show, save)
     [59](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:59)     layers = ["spliced", "unspliced", "ambiguous"]
     [60](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:60) layers_keys = [key for key in layers if key in adata.layers.keys()]
---> [61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61) counts_layers = [sum(adata.layers[key], axis=1) for key in layers_keys]
     [63](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:63) if use_raw:
     [64](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:64)     ikey, obs = "initial_size_", adata.obs

File [~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61), in <listcomp>(.0)
     [59](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:59)     layers = ["spliced", "unspliced", "ambiguous"]
     [60](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:60) layers_keys = [key for key in layers if key in adata.layers.keys()]
---> [61](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:61) counts_layers = [sum(adata.layers[key], axis=1) for key in layers_keys]
     [63](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:63) if use_raw:
     [64](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/plotting/proportions.py:64)     ikey, obs = "initial_size_", adata.obs

File [~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:119](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:119), in sum(a, axis)
    [103](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:103) def sum(a: Union[ndarray, spmatrix], axis: Optional[int] = None) -> ndarray:
    [104](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:104)     """Sum array elements over a given axis.
    [105](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:105) 
    [106](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:106)     Arguments:
   (...)
...
--> [119](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:119)     if a.ndim == 1:
    [120](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:120)         axis = 0
    [122](https://vscode-remote+ssh-002dremote-002b7b22686f73744e616d65223a2241746c6173227d.vscode-resource.vscode-cdn.net/mnt/atlas_local/jonathan/home/projects/Sivan_NASA/scRNA/main/qc/rnavelocity/integration/~/miniconda3/envs/scvelo/lib/python3.9/site-packages/scvelo/core/_arithmetic.py:122)     with warnings.catch_warnings():

AttributeError: 'AnnData' object has no attribute 'ndim'
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?f37c88c8-0d49-41c8-bb31-882d9349a274) or open in a [text editor](command:workbench.action.openLargeOutput?f37c88c8-0d49-41c8-bb31-882d9349a274). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

Wondering if there is some issue from converting my data from a Seurat object into an AnnData object.

Here is my output for package versions

scv.logging.print_versions()

scvelo==0.3.1  scanpy==1.9.8  anndata==0.10.6  loompy==3.0.7  numpy==1.26.4  scipy==1.12.0  matplotlib==3.8.3  sklearn==1.4.1.post1  pandas==2.2.1  
ERROR: XMLRPC request failed [code: -32500]
RuntimeError: PyPI no longer supports 'pip search' (or XML-RPC search). Please use https://pypi.org/search (via a browser) instead. See https://warehouse.pypa.io/api-reference/xml-rpc.html#deprecated-methods for more information.
jjia1 commented 4 months ago

I fixed the issue. I did not realize that I did not set the spliced and unspliced layers equal to the count matrix but rather I had set it as the entire AnnData object.