Fix sparse matrix check and optimize index handling #346
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| if scipy.issparse(adata.X): | ||
| if scipy.sparse.issparse(adata.X): | ||
| df = pd.DataFrame(adata.X.toarray(), columns=adata.var_names) |
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can you please confirm the version requirement for scipy? does it match up with the one stated in the requirements.txt file?
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I have confirmed that the requirements are met. scipy.sparse.issparse is supported in v1.0.0(https://github.com/scipy/scipy/blob/11509c4a98edded6c59423ac44ca1b7f28fba1fd/scipy/sparse/base.py#L1231)
| _spatial = np.array(df2.index.to_list()) | ||
| _idx = [str(i[0]) + "_" + str(i[1]) for i in df2.index.to_list()] | ||
| df2.index = _idx | ||
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note that f2.index.to_list() may be a tuple (for x/y dimensions). what you have assumes the index is just a numeric value
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The index is come from the spatial information so it's the numeric value
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hmm, it should not be a couple of x, y coordinates?
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Oh, I misunderstood. It is a list composed of tuples (x, y), but the code here can convert it into an array with shape (n, 2).
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Fig bug #345