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raphael-group / STARCH

Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
MIT License
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How to solve this problem? #3

Open hzaumsq opened 3 years ago

hzaumsq commented 3 years ago

INFO:root:preprocess 12720 2425 (12720, 2425) INFO:root:done preprocessing... True INFO:root:getting spot network... INFO:root:initializing labels... Traceback (most recent call last): File "run_STARCH.py", line 34, in operator = STARCH(i,n_clusters=n_clusters,num_states=3,normal_spots=normal_spots,beta_spots = beta_spot,nthreads=nthreads,gene_mapping_file_name=gene_mapping_file_name) File "/beegfs/home/msq/St/CNV/STARCH-master/STARCH.py", line 133, in init self.initialize_labels() File "/beegfs/home/msq/St/CNV/STARCH-master/STARCH.py", line 478, in initialize_labels km = KMeans(n_clusters=self.n_clusters).fit(dat.T) File "/beegfs/home/msq/miniconda3/envs/python2/lib/python2.7/site-packages/sklearn/cluster/kmeans.py", line 974, in fit return_n_iter=True) File "/beegfs/home/msq/miniconda3/envs/python2/lib/python2.7/site-packages/sklearn/cluster/kmeans.py", line 314, in k_means order=order, copy=copy_x) File "/beegfs/home/msq/miniconda3/envs/python2/lib/python2.7/site-packages/sklearn/utils/validation.py", line 573, in check_array allow_nan=force_all_finite == 'allow-nan') File "/beegfs/home/msq/miniconda3/envs/python2/lib/python2.7/site-packages/sklearn/utils/validation.py", line 56, in _assert_all_finite raise ValueError(msg_err.format(type_err, X.dtype)) ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

hzaumsq commented 3 years ago

I use the 10x spatial result The coed : runSTARCH.py -i ../cnv/ -t 20 --output yy --n_clusters 3 --outdir ./test

hzaumsq commented 3 years ago

Also could you provide the more details explanation of results