animate error

[PietroD]

I am trying animate function but I get an error:

sm.hl.animate(adata_a, x_coordinate = 'X_centroid', y_coordinate = 'Y_centroid')

KeyError                                  Traceback (most recent call last)
Cell In[29], [line 6](vscode-notebook-cell:?execution_count=29&line=6)
      [3](vscode-notebook-cell:?execution_count=29&line=3) adata_a.obs['Y_centroid'] = adata_a.obsm['Y_centroid'].flatten()
      [5](vscode-notebook-cell:?execution_count=29&line=5) # Basic animation with default UMAP and spatial coordinates
----> [6](vscode-notebook-cell:?execution_count=29&line=6) sm.hl.animate(adata_a, x_coordinate = 'X_centroid', y_coordinate = 'Y_centroid')
      [8](vscode-notebook-cell:?execution_count=29&line=8) # sm.hl.animate(adata_a, 
      [9](vscode-notebook-cell:?execution_count=29&line=9) #               embedding='umap', 
     [10](vscode-notebook-cell:?execution_count=29&line=10) #               x_coordinate='X_centroid', 
   (...)
     [33](vscode-notebook-cell:?execution_count=29&line=33) # sm.hl.animate(adata, color='condition', palette={'Control': '#1f77b4', 'Treated': '#ff7f0e'}, 
     [34](vscode-notebook-cell:?execution_count=29&line=34) #         subset='image_01', interval=100, save_animation='custom_animation.gif')

File /opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:267, in animate(adata, color, palette, embedding, x_coordinate, y_coordinate, flip_y, imageid, subset, layer, use_raw, log, subsample, random_state, n_frames, interval, reverse, final_frame, s, alpha, cmap, tight_layout, plot_legend, title, fontsize, watermark, figsize, pltStyle, verbose, save_animation, **kwargs)
    [265](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:265) # extract the spaces
    [266](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:266) e1 = final_data[['umap-1', 'umap-2']].values.astype(float)
--> [267](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:267) e2 = final_data[[x_coordinate,y_coordinate]].values.astype(float)
    [270](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:270) # rescale to same co-ordinates system
    [271](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/scimap/helpers/animate.py:271) e1[:, 0] -= (max(e1[:, 0]) + min(e1[:, 0])) / 2

File /opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/frame.py:4108, in DataFrame.__getitem__(self, key)
   [4106](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/frame.py:4106)     if is_iterator(key):
   [4107](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/frame.py:4107)         key = list(key)
-> [4108](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/frame.py:4108)     indexer = self.columns._get_indexer_strict(key, "columns")[1]
   [4110](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/frame.py:4110) # take() does not accept boolean indexers
...
-> [6249](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/indexes/base.py:6249)         raise KeyError(f"None of [{key}] are in the [{axis_name}]")
   [6251](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/indexes/base.py:6251)     not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique())
   [6252](https://file+.vscode-resource.vscode-cdn.net/opt/homebrew/Caskroom/miniforge/base/envs/akoya/lib/python3.10/site-packages/pandas/core/indexes/base.py:6252)     raise KeyError(f"{not_found} not in index")

KeyError: "None of [Index(['X_centroid', 'Y_centroid'], dtype='object')] are in the [columns]"

Even if I have both 'X_centroid' and 'Y_centroid' in my adata.obs:

Thanks

[ajitjohnson]

hmm can you share your adata. If it is large, please subset it to about 10,000 cells.

[PietroD]

Subsetted to a thousand cells but got the same error

[jmkotah]

Hi @ajitjohnson and the scimap team, thanks for this package!

I was trying out your package to visualize UMAPs and spatial plots and encountered the same problem.

I believe the error comes from lines 248-252 of the source code as available here:

    # combine color data with umap coordinates
    if color_data is not None:
        final_data = pd.concat([umap_coordinates, real_coordinates, color_data], axis=1)
    else:
        final_data = umap_coordinates

Specifically, if there is no variable specified in the color argument, the 'final_data' df takes only the UMAP coords, and not the spatial coordinates. Therefore the rest of the code bugs out as it tries to find the x/y centroid columns where it is not available.

In practice of course one would not plot this without specifying how to color all the points, but thought I would let you know.

Have a nice day!