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Why we cannot tranfer adata along with functions? #2030

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hyjforesight opened this issue Nov 1, 2021 · 1 comment
Closed

Why we cannot tranfer adata along with functions? #2030

hyjforesight opened this issue Nov 1, 2021 · 1 comment

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@hyjforesight
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hyjforesight commented Nov 1, 2021 •
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Hello all,
For these 2 functions,
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)
the authors make inplace=True as default.

Because I want to tranfer the output into an variable, I change these functions to

a=sc.pp.filter_cells(adata, min_genes=200, inplace=False)
sc.pp.filter_genes(a, min_cells=3, inplace=False)

but it creates errors and the output of a is NoType:

aceback (most recent call last):
File “C:\Users\Yuanjian\AppData\Local\Programs\Python\Python36\lib\site-packages\IPython\core\interactiveshell.py”, line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File “”, line 2, in
sc.pp.filter_genes(a, min_cells=3, inplace=False) # exclude genes only expressed in <3 cells
File “C:\Users\Yuanjian\AppData\Local\Programs\Python\Python36\lib\site-packages\scanpy\preprocessing_simple.py”, line 259, in filter_genes
X if min_cells is None and max_cells is None else X > 0, axis=0

Does anybody know why inplace=False doesn’t work?
Thanks!
Best,
YJ
@ivirshup
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I would agree the results of sc.pp.filter_genes(..., inplace=False) are not the most intuitive. Instead of returning a filtered anndata, it returns which cells would have been filtered and the stats which were used to make this decision. This is documented under the Returns section for these functions.

What you might want is

mask, _ = sc.pp.filter_cells(adata, min_genes=200, inplace=False)
a = adata[mask].copy()

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@ivirshup @hyjforesight