Help with error scanpy

Question

[Chris]

Hi all,

I try to do annotation for single cell using scanpy and got this error that I didn't found on the internet:
Would you please have a suggestion? Code is adapt from https://github.com/bnsreenu/python_for_microscopists/blob/master/326_Cell_type_annotation_for_single_cell_RNA_seq_data%E2%80%8B.ipynb Thank you so much!

sc.pl.umap(adata)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Input In [34], in <cell line: 1>()
----> 1 sc.pl.umap(adata)

File ~/.local/lib/python3.9/site-packages/scanpy/plotting/_tools/scatterplots.py:668, in umap(adata, **kwargs)
    609 @_wraps_plot_scatter
    610 @_doc_params(
    611     adata_color_etc=doc_adata_color_etc,
   (...)
    615 )
    616 def umap(adata, **kwargs) -> Union[Axes, List[Axes], None]:
    617     """\
    618     Scatter plot in UMAP basis.
    619 
   (...)
    666     tl.umap
    667     """
--> 668     return embedding(adata, 'umap', **kwargs)

File ~/.local/lib/python3.9/site-packages/scanpy/plotting/_tools/scatterplots.py:162, in embedding(adata, basis, color, gene_symbols, use_raw, sort_order, edges, edges_width, edges_color, neighbors_key, arrows, arrows_kwds, groups, components, dimensions, layer, projection, scale_factor, color_map, cmap, palette, na_color, na_in_legend, size, frameon, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, colorbar_loc, vmax, vmin, vcenter, norm, add_outline, outline_width, outline_color, ncols, hspace, wspace, title, show, save, ax, return_fig, **kwargs)
    160     else:
    161         cmap = color_map
--> 162 cmap = copy(colormaps.get_cmap(cmap))
    163 cmap.set_bad(na_color)
    164 kwargs["cmap"] = cmap

AttributeError: 'ColormapRegistry' object has no attribute 'get_cmap'

[bk11]

You probably need to do following again.

conda install -c conda-forge scanpy python-igraph leidenalg

If it does not work, you may need to install whole conda. See below-

https://discourse.scverse.org/t/error-when-draw-umap-object-has-no-attribute-get-cmap/1726/3

[Chris]

Seem this installation precess takes a long time. Still waiting. Thank you so much!

[Ram]

Switch to mamba. It's orders of magnitude faster.

Answer 1

[Jorge]

Hi,

I had the same issue, and I resolved it as follows:

1. I replaced the problematic line in the ~/.local/lib/python3.8/site-packages/scanpy/plotting/_tools/scatterplots.py file (line 162) with the following code:

    cmap = copy(plt.cm.get_cmap(cmap))
   

   Since 'plt' was not loaded in the file, I added the following import statement at the top of the same file to import Matplotlib as 'plt':

    import matplotlib.pyplot as plt
   

2. After making these changes, I saved the file.

3. To apply the fix, I restarted my Jupyter Notebook or the Python environment where I was using Scanpy.

After following these steps, the issue was resolved, and my process executed correctly.

[Chris]

It worked! Thank you so much!

[sredemption]

Thank you for these steps!