Open DRSEI opened 1 year ago
I keep getting this error and i ' m not sure what is the problem . Appriciated your helps .
Package was installed.
`--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In [75], line 1 ----> 1 cdata = sc.external.pp.mnn_correct(alldata['CID3586'],alldata['CID3838'],alldata['CID3921'], 2 alldata['CID3941'], 3 svd_dim = 50, batch_key = 'patientID', save_raw = True, var_subset = var_genes)
File /opt/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scanpy/external/pp/_mnn_correct.py:135, in mnn_correct(var_index, var_subset, batch_key, index_unique, batch_categories, k, sigma, cos_norm_in, cos_norm_out, svd_dim, var_adj, compute_angle, mnn_order, svd_mode, do_concatenate, save_raw, n_jobs, *datas, *kwargs) 129 raise ImportError( 130 'Please install the package mnnpy ' 131 '(https://github.com/chriscainx/mnnpy). ' 132 ) 134 n_jobs = settings.n_jobs if n_jobs is None else n_jobs --> 135 datas, mnn_list, angle_list = mnn_correct( 136 datas, 137 var_index=var_index, 138 var_subset=var_subset, 139 batch_key=batch_key, 140 index_unique=index_unique, 141 batch_categories=batch_categories, 142 k=k, 143 sigma=sigma, 144 cos_norm_in=cos_norm_in, 145 cos_norm_out=cos_norm_out, 146 svd_dim=svd_dim, ... File _ckdtree.pyx:786, in scipy.spatial._ckdtree.cKDTree.query()
File _ckdtree.pyx:390, in scipy.spatial._ckdtree.get_num_workers()
TypeError: Unexpected keyword argument {'n_jobs': 20}`
See Issue #49
I keep getting this error and i ' m not sure what is the problem . Appriciated your helps .
Package was installed.
`--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In [75], line 1 ----> 1 cdata = sc.external.pp.mnn_correct(alldata['CID3586'],alldata['CID3838'],alldata['CID3921'], 2 alldata['CID3941'], 3 svd_dim = 50, batch_key = 'patientID', save_raw = True, var_subset = var_genes)
File /opt/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scanpy/external/pp/_mnn_correct.py:135, in mnn_correct(var_index, var_subset, batch_key, index_unique, batch_categories, k, sigma, cos_norm_in, cos_norm_out, svd_dim, var_adj, compute_angle, mnn_order, svd_mode, do_concatenate, save_raw, n_jobs, *datas, *kwargs) 129 raise ImportError( 130 'Please install the package mnnpy ' 131 '(https://github.com/chriscainx/mnnpy). ' 132 ) 134 n_jobs = settings.n_jobs if n_jobs is None else n_jobs --> 135 datas, mnn_list, angle_list = mnn_correct( 136 datas, 137 var_index=var_index, 138 var_subset=var_subset, 139 batch_key=batch_key, 140 index_unique=index_unique, 141 batch_categories=batch_categories, 142 k=k, 143 sigma=sigma, 144 cos_norm_in=cos_norm_in, 145 cos_norm_out=cos_norm_out, 146 svd_dim=svd_dim, ... File _ckdtree.pyx:786, in scipy.spatial._ckdtree.cKDTree.query()
File _ckdtree.pyx:390, in scipy.spatial._ckdtree.get_num_workers()
TypeError: Unexpected keyword argument {'n_jobs': 20}`