Issues running test.py about pywgcna HOT 5 CLOSED

I suggest you follow Quick_Start.ipynb on the test data. To make sure your data is inserted in PyWGCNA correctly, try to look at pyWGCNA_5xFAD.geneExpr.to_df() to make sure your gene_ids are stored as an index and your sample names are stored as a column.

Also please make sure you have the latest version of the package

at this time the latest version is v0.8.6 so you can run pip install PyWGCNA==v0.8.6

from pywgcna.

Hi,
I installed the latest version and am having issues loading the file.

ValueError Traceback (most recent call last)
/Users/yashsondhi/Dropbox/diel-rna-seq/Sondhi_etal_rna_seq_MS/scripts/PyWGCNA/tutorials/Quick_Start.ipynb Cell 2' in <cell line: 5>()
3 os.getcwd()
4 geneExp = '5xFAD_paper/expressionList_sorted.csv'
----> 5 pyWGCNA_5xFAD = PyWGCNA.WGCNA(name='5xFAD', species='mouse', geneExpPath=geneExp, save=True)
6 pyWGCNA_5xFAD.geneExpr.to_df().head(5)

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/PyWGCNA/wgcna.py:126, in WGCNA.init(self, name, TPMcutoff, powers, RsquaredCut, MeanCut, networkType, TOMType, minModuleSize, naColor, cut, MEDissThres, species, level, anndata, geneExp, geneExpPath, sep, save, outputPath)
116 def init(self, name='WGCNA',
117 TPMcutoff=1,
118 powers=None, RsquaredCut=0.9, MeanCut=100,
(...)
123 geneExpPath=None, sep=',',
124 save=False, outputPath=None):
--> 126 super().init(species=species, level=level, anndata=anndata, geneExp=geneExp,
127 geneExpPath=geneExpPath, sep=sep)
129 if powers is None:
130 powers = list(range(1, 11)) + list(range(11, 21, 2))

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/PyWGCNA/geneExp.py:69, in GeneExp.init(self, species, level, anndata, geneExp, geneExpPath, sep)
66 # drop sample id columns
67 expressionList = expressionList.drop([expressionList.columns[0]], axis=1)
---> 69 self.geneExpr = ad.AnnData(X=expressionList, obs=sampleInfo, var=geneInfo)

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/anndata/_core/anndata.py:291, in AnnData.init(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
289 self._init_as_view(X, oidx, vidx)
290 else:
--> 291 self._init_as_actual(
292 X=X,
293 obs=obs,
294 var=var,
295 uns=uns,
296 obsm=obsm,
297 varm=varm,
298 raw=raw,
299 layers=layers,
300 dtype=dtype,
301 shape=shape,
302 obsp=obsp,
303 varp=varp,
304 filename=filename,
305 filemode=filemode,
306 )

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/anndata/_core/anndata.py:435, in AnnData._init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
433 elif not isinstance(X.columns, pd.RangeIndex):
434 x_indices.append(("var", "columns", X.columns))
--> 435 X = ensure_df_homogeneous(X, "X")
437 # ----------------------------------------------------------------------
438 # actually process the data
439 # ----------------------------------------------------------------------
440
441 # check data type of X
442 if X is not None:

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/anndata/utils.py:139, in ensure_df_homogeneous(df, name)
134 def ensure_df_homogeneous(
135 df: pd.DataFrame, name: str
136 ) -> Union[np.ndarray, sparse.csr_matrix]:
137 # TODO: rename this function, I would not expect this to return a non-dataframe
138 if all(isinstance(dt, pd.SparseDtype) for dt in df.dtypes):
--> 139 arr = df.sparse.to_coo().tocsr()
140 else:
141 arr = df.to_numpy()

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/pandas/core/arrays/sparse/accessor.py:337, in SparseFrameAccessor.to_coo(self)
334 import_optional_dependency("scipy")
335 from scipy.sparse import coo_matrix
--> 337 dtype = find_common_type(self._parent.dtypes.to_list())
338 if isinstance(dtype, SparseDtype):
339 dtype = dtype.subtype

File ~/opt/anaconda3/envs/wgcna/lib/python3.9/site-packages/pandas/core/dtypes/cast.py:1807, in find_common_type(types)
1790 """
1791 Find a common data type among the given dtypes.
1792
(...)
1804
1805 """
1806 if not types:
-> 1807 raise ValueError("no types given")
1809 first = types[0]
1811 # workaround for find_common_type([np.dtype('datetime64[ns]')] * 2)
1812 # => object

ValueError: no types given

from pywgcna.

Hi again,

Can you please check that you have the latest version of the input files, as well?

Unfotunelty, I can not reproduce your error but if you can tell me which version of anndata you used it might be helpful

from pywgcna.

I got a same issue like this:

Traceback (most recent call last):
File "WGCNA.py", line 3, in
pyWGCNA_5xFAD = PyWGCNA.WGCNA(name='5xFAD',
File "/home/tanygyun/.local/lib/python3.8/site-packages/PyWGCNA/wgcna.py", line 126, in init
super().init(species=species, level=level, anndata=anndata, geneExp=geneExp,
File "/home/tanygyun/.local/lib/python3.8/site-packages/PyWGCNA/geneExp.py", line 69, in init
self.geneExpr = ad.AnnData(X=expressionList, obs=sampleInfo, var=geneInfo)
File "/home/tanygyun/.local/lib/python3.8/site-packages/anndata/_core/anndata.py", line 291, in init
self._init_as_actual(
File "/home/tanygyun/.local/lib/python3.8/site-packages/anndata/_core/anndata.py", line 435, in _init_as_actual
X = ensure_df_homogeneous(X, "X")
File "/home/tanygyun/.local/lib/python3.8/site-packages/anndata/utils.py", line 139, in ensure_df_homogeneous
arr = df.sparse.to_coo().tocsr()
File "/home/tanygyun/.local/lib/python3.8/site-packages/pandas/core/arrays/sparse/accessor.py", line 337, in to_coo
dtype = find_common_type(self._parent.dtypes.to_list())
File "/home/tanygyun/.local/lib/python3.8/site-packages/pandas/core/dtypes/cast.py", line 1807, in find_common_type
raise ValueError("no types given")
ValueError: no types given

from pywgcna.

@1391794753 can you send me an example of the data you used it?

from pywgcna.