Error for clf.fit #158
Description
Hi!Thank you for your tool!
But when i execute this commend
doublets = clf.fit(adata.X).predict(p_thresh=1e-16, voter_thresh=0.5)
an error below:
{
"name": "AttributeError",
"message": "'csr_matrix' object has no attribute 'A'",
"stack": "---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[37], line 1
----> 1 adatas_pp = [pp(ad) for ad in adatas]
Cell In[37], line 1, in (.0)
----> 1 adatas_pp = [pp(ad) for ad in adatas]
Cell In[36], line 11, in pp(adata)
9 adata.uns['cells_removed'] = sum(bool_vector)
10 # 检测双重细胞
---> 11 doublets = clf.fit(adata.X).predict(p_thresh=1e-16, voter_thresh=0.5)
12 doublet_score = clf.doublet_score()
13 # 保存双重细胞信息
File ~/miniconda3/envs/scanpy/lib/python3.10/site-packages/doubletdetection/doubletdetection.py:208, in BoostClassifier.fit(self, raw_counts)
206 if self.verbose:
207 print("Iteration {:3}/{}".format(i + 1, self.n_iters))
--> 208 self.all_scores_[i], self.all_log_p_values_[i] = self.one_fit()
209 all_communities[i] = self.communities
210 all_parents.append(self.parents_)
File ~/miniconda3/envs/scanpy/lib/python3.10/site-packages/doubletdetection/doubletdetection.py:308, in BoostClassifier._one_fit(self)
306 scaled_aug_counts = aug_counts * np.median(aug_lib_size)
307 if self.pseudocount != 1:
--> 308 aug_counts = np.log(scaled_aug_counts.A + 0.1)
309 else:
310 aug_counts = np.log1p(scaled_aug_counts)
AttributeError: 'csr_matrix' object has no attribute 'A'"
}
But your update shows that it supports csr_matrix!Looking foward to your reply!Thanks!