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ImplicitModificationWarning when aggregating data #11

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LuLeom opened this issue Sep 6, 2024 · 0 comments
Open

ImplicitModificationWarning when aggregating data #11

LuLeom opened this issue Sep 6, 2024 · 0 comments
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bug Something isn't working

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@LuLeom
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LuLeom commented Sep 6, 2024

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Hello,

This is not really a major bug, but I still wanted to report some warnings when using the fs.pp.aggregate_flowframes() function:

aggregated_data= fs.pp.aggregate_flowframes(
    filenames=fcs_files_list, #A list with all my .fcs file paths
    c_total=80000,
)

This results in the following warnings:

``bash [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/flowsom/pp/fcs_functions.py:49): ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. f.obs["Original_ID"] = np.array(ids, dtype=np.float32) [/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/anndata/_core/anndata.py:1754](https://file+.vscode-resource.vscode-cdn.net/Users/lucal/miniconda3/envs/cyto/lib/python3.12/site-packages/anndata/_core/anndata.py:1754): UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") ```
Despite the warnings, the function seems to work as usual.

Best

@LuLeom LuLeom added the bug Something isn't working label Sep 6, 2024
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