Running example code from Augur plot (e.g. scatterplot) causes a lot of warnings from the original Augur module being printed out:
This line in particular:
h_adata, h_results = ag_rfc.predict(loaded_data, subsample_size=20, n_threads=4)
causes:
/fs/gpfs41/lv07/fileset03/home/g_mann/namsaraeva/Packages/pertpy/pertpy/tools/_augur.py:238: FutureWarning: Use anndata.concat instead of AnnData.concatenate, AnnData.concatenate is deprecated and will be removed in the future. See the tutorial for concat at: https://anndata.readthedocs.io/en/latest/concatenation.html subsample = AnnData.concatenate(*label_subsamples, index_unique=None)
and
/fs/home/namsaraeva/miniconda3/envs/pertpy/lib/python3.10/site-packages/sklearn/metrics/_scorer.py:548: FutureWarning: The needs_threshold and needs_proba parameter are deprecated in version 1.4 and will be removed in 1.6. You can either let response_method be None or set it to predict to preserve the same behaviour.
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Running example code from Augur plot (e.g.
scatterplot) causes a lot of warnings from the original Augur module being printed out:This line in particular:
h_adata, h_results = ag_rfc.predict(loaded_data, subsample_size=20, n_threads=4)causes:
/fs/gpfs41/lv07/fileset03/home/g_mann/namsaraeva/Packages/pertpy/pertpy/tools/_augur.py:238: FutureWarning: Use anndata.concat instead of AnnData.concatenate, AnnData.concatenate is deprecated and will be removed in the future. See the tutorial for concat at: https://anndata.readthedocs.io/en/latest/concatenation.html subsample = AnnData.concatenate(*label_subsamples, index_unique=None)and
/fs/home/namsaraeva/miniconda3/envs/pertpy/lib/python3.10/site-packages/sklearn/metrics/_scorer.py:548: FutureWarning: The needs_threshold and needs_proba parameter are deprecated in version 1.4 and will be removed in 1.6. You can either let response_method be None or set it to predict to preserve the same behaviour.Version information
No response