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hello,you really do a good job,but i met some trouble,could ypu tell me how to fix it.and the question is as followed:
ValueError Traceback (most recent call last)
in
----> 1 adata=desc.train(adata,
2 dims=[adata.shape[1],64,32],
3 tol=0.005,
4 n_neighbors=10,
5 batch_size=256,
~/anaconda3/envs/R_env/lib/python3.8/site-packages/desc/models/desc.py in train_single(data, dims, alpha, tol, init, louvain_resolution, n_neighbors, pretrain_epochs, batch_size, activation, actincenter, drop_rate_SAE, is_stacked, use_earlyStop, use_ae_weights, save_encoder_weights, save_encoder_step, save_dir, max_iter, epochs_fit, num_Cores, num_Cores_tsne, use_GPU, GPU_id, random_seed, verbose, do_tsne, learning_rate, perplexity, do_umap, kernel_clustering)
162 if do_tsne:
163 num_Cores_tsne=int(num_Cores_tsne) if total_cpu>int(num_Cores_tsne) else int(math.ceil(total_cpu/2))
--> 164 sc.tl.tsne(adata,use_rep="X_Embeded_z"+str(louvain_resolution),learning_rate=learning_rate,perplexity=perplexity,n_jobs=num_Cores_tsne)
165 adata.obsm["X_tsne"+str(louvain_resolution)]=adata.obsm["X_tsne"].copy()
166 print('tsne finished and added X_tsne'+str(louvain_resolution),' into the umap coordinates (adata.obsm)\n')
~/anaconda3/envs/R_env/lib/python3.8/site-packages/scanpy/tools/_tsne.py in tsne(adata, n_pcs, use_rep, perplexity, early_exaggeration, learning_rate, random_state, use_fast_tsne, n_jobs, copy)
113 tsne = TSNE(**params_sklearn)
114 logg.info(' using sklearn.manifold.TSNE with a fix by D. DeTomaso')
--> 115 X_tsne = tsne.fit_transform(X)
116 # update AnnData instance
117 adata.obsm['X_tsne'] = X_tsne # annotate samples with tSNE coordinates
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/t_sne.py in fit_transform(self, X, y)
889 Embedding of the training data in low-dimensional space.
890 """
--> 891 embedding = self.fit(X)
892 self.embedding = embedding
893 return self.embedding
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py in _fit(self, X, skip_num_points)
667 raise ValueError("'angle' must be between 0.0 - 1.0")
668 if self.method == 'barnes_hut':
--> 669 X = self._validate_data(X, accept_sparse=['csr'],
670 ensure_min_samples=2,
671 dtype=[np.float32, np.float64])
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/base.py in _validate_data(self, X, y, reset, validate_separately, **check_params)
418 f"requires y to be passed, but the target y is None."
419 )
--> 420 X = check_array(X, **check_params)
421 out = X
422 else:
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in inner_f(*args, **kwargs)
70 FutureWarning)
71 kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 72 return f(**kwargs)
73 return inner_f
74
hello,you really do a good job,but i met some trouble,could ypu tell me how to fix it.and the question is as followed:
ValueError Traceback (most recent call last)
in
----> 1 adata=desc.train(adata,
2 dims=[adata.shape[1],64,32],
3 tol=0.005,
4 n_neighbors=10,
5 batch_size=256,
~/anaconda3/envs/R_env/lib/python3.8/site-packages/desc/models/desc.py in train(data, dims, alpha, tol, init, louvain_resolution, n_neighbors, pretrain_epochs, batch_size, activation, actincenter, drop_rate_SAE, is_stacked, use_earlyStop, use_ae_weights, save_encoder_weights, save_encoder_step, save_dir, max_iter, epochs_fit, num_Cores, num_Cores_tsne, use_GPU, GPU_id, random_seed, verbose, do_tsne, learning_rate, perplexity, do_umap, kernel_clustering)
301 print("Start to process resolution=",str(resolution))
302 use_ae_weights=use_ae_weights if ith==0 else True
--> 303 res=train_single(data=data,
304 dims=dims,
305 alpha=alpha,
~/anaconda3/envs/R_env/lib/python3.8/site-packages/desc/models/desc.py in train_single(data, dims, alpha, tol, init, louvain_resolution, n_neighbors, pretrain_epochs, batch_size, activation, actincenter, drop_rate_SAE, is_stacked, use_earlyStop, use_ae_weights, save_encoder_weights, save_encoder_step, save_dir, max_iter, epochs_fit, num_Cores, num_Cores_tsne, use_GPU, GPU_id, random_seed, verbose, do_tsne, learning_rate, perplexity, do_umap, kernel_clustering)
162 if do_tsne:
163 num_Cores_tsne=int(num_Cores_tsne) if total_cpu>int(num_Cores_tsne) else int(math.ceil(total_cpu/2))
--> 164 sc.tl.tsne(adata,use_rep="X_Embeded_z"+str(louvain_resolution),learning_rate=learning_rate,perplexity=perplexity,n_jobs=num_Cores_tsne)
165 adata.obsm["X_tsne"+str(louvain_resolution)]=adata.obsm["X_tsne"].copy()
166 print('tsne finished and added X_tsne'+str(louvain_resolution),' into the umap coordinates (adata.obsm)\n')
~/anaconda3/envs/R_env/lib/python3.8/site-packages/scanpy/tools/_tsne.py in tsne(adata, n_pcs, use_rep, perplexity, early_exaggeration, learning_rate, random_state, use_fast_tsne, n_jobs, copy)
113 tsne = TSNE(**params_sklearn)
114 logg.info(' using sklearn.manifold.TSNE with a fix by D. DeTomaso')
--> 115 X_tsne = tsne.fit_transform(X)
116 # update AnnData instance
117 adata.obsm['X_tsne'] = X_tsne # annotate samples with tSNE coordinates
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/t_sne.py in fit_transform(self, X, y)
889 Embedding of the training data in low-dimensional space.
890 """
--> 891 embedding = self.fit(X)
892 self.embedding = embedding
893 return self.embedding
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py in _fit(self, X, skip_num_points)
667 raise ValueError("'angle' must be between 0.0 - 1.0")
668 if self.method == 'barnes_hut':
--> 669 X = self._validate_data(X, accept_sparse=['csr'],
670 ensure_min_samples=2,
671 dtype=[np.float32, np.float64])
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/base.py in _validate_data(self, X, y, reset, validate_separately, **check_params)
418 f"requires y to be passed, but the target y is None."
419 )
--> 420 X = check_array(X, **check_params)
421 out = X
422 else:
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in inner_f(*args, **kwargs)
70 FutureWarning)
71 kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 72 return f(**kwargs)
73 return inner_f
74
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in check_array(array, accept_sparse, accept_large_sparse, dtype, order, copy, force_all_finite, ensure_2d, allow_nd, ensure_min_samples, ensure_min_features, estimator)
642
643 if force_all_finite:
--> 644 _assert_all_finite(array,
645 allow_nan=force_all_finite == 'allow-nan')
646
~/anaconda3/envs/R_env/lib/python3.8/site-packages/sklearn/utils/validation.py in _assert_all_finite(X, allow_nan, msg_dtype)
94 not allow_nan and not np.isfinite(X).all()):
95 type_err = 'infinity' if allow_nan else 'NaN, infinity'
---> 96 raise ValueError(
97 msg_err.format
98 (type_err,
ValueError: Input contains NaN, infinity or a value too large for dtype('float32').
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