ValueError Traceback (most recent call last)
Cell In[7], line 1
----> 1 pyWGCNA_5xFAD.analyseWGCNA(show=False)
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/PyWGCNA/wgcna.py:470, in WGCNA.analyseWGCNA(self, order, geneList, show, alternative)
468 else:
469 for module in modules:
--> 470 self.barplotModuleEigenGene(module, metadata, colorBar=metadata[-1], show=show)
471 print("\tDone..\n")
473 if self.save:
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/PyWGCNA/wgcna.py:3133, in WGCNA.barplotModuleEigenGene(self, moduleName, metadata, combine, colorBar, show)
3131 else:
3132 palette = cat[[colorBar]].copy()
-> 3133 palette[[colorBar]] = palette[[colorBar]].astype('int')
3134 palette[colorBar] = palette[colorBar].apply(lambda x: mcolors.to_hex(self.metadataColors[colorBar].to_rgba(float(x))) if pd.notna(x) else "#FFFFFF")
3135 palette = palette[colorBar].values
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/generic.py:6662, in NDFrame.astype(self, dtype, copy, errors)
6656 results = [
6657 ser.astype(dtype, copy=copy, errors=errors) for _, ser in self.items()
6658 ]
6660 else:
6661 # else, only a single dtype is given
-> 6662 new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
6663 res = self._constructor_from_mgr(new_data, axes=new_data.axes)
6664 return res.finalize(self, method="astype")
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/managers.py:430, in BaseBlockManager.astype(self, dtype, copy, errors)
427 elif using_copy_on_write():
428 copy = False
--> 430 return self.apply(
431 "astype",
432 dtype=dtype,
433 copy=copy,
434 errors=errors,
435 using_cow=using_copy_on_write(),
436 )
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/managers.py:363, in BaseBlockManager.apply(self, f, align_keys, **kwargs)
361 applied = b.apply(f, **kwargs)
362 else:
--> 363 applied = getattr(b, f)(**kwargs)
364 result_blocks = extend_blocks(applied, result_blocks)
366 out = type(self).from_blocks(result_blocks, self.axes)
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/blocks.py:784, in Block.astype(self, dtype, copy, errors, using_cow, squeeze)
781 raise ValueError("Can not squeeze with more than one column.")
782 values = values[0, :] # type: ignore[call-overload]
--> 784 new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
786 new_values = maybe_coerce_values(new_values)
788 refs = None
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:237, in astype_array_safe(values, dtype, copy, errors)
234 dtype = dtype.numpy_dtype
236 try:
--> 237 new_values = astype_array(values, dtype, copy=copy)
238 except (ValueError, TypeError):
239 # e.g. _astype_nansafe can fail on object-dtype of strings
240 # trying to convert to float
241 if errors == "ignore":
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:182, in astype_array(values, dtype, copy)
179 values = values.astype(dtype, copy=copy)
181 else:
--> 182 values = _astype_nansafe(values, dtype, copy=copy)
184 # in pandas we don't store numpy str dtypes, so convert to object
185 if isinstance(dtype, np.dtype) and issubclass(values.dtype.type, str):
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:133, in _astype_nansafe(arr, dtype, copy, skipna)
129 raise ValueError(msg)
131 if copy or arr.dtype == object or dtype == object:
132 # Explicit copy, or required since NumPy can't view from / to object.
--> 133 return arr.astype(dtype, copy=True)
135 return arr.astype(dtype, copy=copy)
ValueError: invalid literal for int() with base 10: '5xFADHEMI'
When run the pyWGCNA_5xFAD.analyseWGCNA(show=False)
Why the official codes have the error?
ValueError Traceback (most recent call last)
Cell In[7], line 1
----> 1 pyWGCNA_5xFAD.analyseWGCNA(show=False)
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/PyWGCNA/wgcna.py:470, in WGCNA.analyseWGCNA(self, order, geneList, show, alternative)
468 else:
469 for module in modules:
--> 470 self.barplotModuleEigenGene(module, metadata, colorBar=metadata[-1], show=show)
471 print("\tDone..\n")
473 if self.save:
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/PyWGCNA/wgcna.py:3133, in WGCNA.barplotModuleEigenGene(self, moduleName, metadata, combine, colorBar, show)
3131 else:
3132 palette = cat[[colorBar]].copy()
-> 3133 palette[[colorBar]] = palette[[colorBar]].astype('int')
3134 palette[colorBar] = palette[colorBar].apply(lambda x: mcolors.to_hex(self.metadataColors[colorBar].to_rgba(float(x))) if pd.notna(x) else "#FFFFFF")
3135 palette = palette[colorBar].values
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/generic.py:6662, in NDFrame.astype(self, dtype, copy, errors)
6656 results = [
6657 ser.astype(dtype, copy=copy, errors=errors) for _, ser in self.items()
6658 ]
6660 else:
6661 # else, only a single dtype is given
-> 6662 new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
6663 res = self._constructor_from_mgr(new_data, axes=new_data.axes)
6664 return res.finalize(self, method="astype")
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/managers.py:430, in BaseBlockManager.astype(self, dtype, copy, errors)
427 elif using_copy_on_write():
428 copy = False
--> 430 return self.apply(
431 "astype",
432 dtype=dtype,
433 copy=copy,
434 errors=errors,
435 using_cow=using_copy_on_write(),
436 )
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/managers.py:363, in BaseBlockManager.apply(self, f, align_keys, **kwargs)
361 applied = b.apply(f, **kwargs)
362 else:
--> 363 applied = getattr(b, f)(**kwargs)
364 result_blocks = extend_blocks(applied, result_blocks)
366 out = type(self).from_blocks(result_blocks, self.axes)
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/internals/blocks.py:784, in Block.astype(self, dtype, copy, errors, using_cow, squeeze)
781 raise ValueError("Can not squeeze with more than one column.")
782 values = values[0, :] # type: ignore[call-overload]
--> 784 new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
786 new_values = maybe_coerce_values(new_values)
788 refs = None
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:237, in astype_array_safe(values, dtype, copy, errors)
234 dtype = dtype.numpy_dtype
236 try:
--> 237 new_values = astype_array(values, dtype, copy=copy)
238 except (ValueError, TypeError):
239 # e.g. _astype_nansafe can fail on object-dtype of strings
240 # trying to convert to float
241 if errors == "ignore":
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:182, in astype_array(values, dtype, copy)
179 values = values.astype(dtype, copy=copy)
181 else:
--> 182 values = _astype_nansafe(values, dtype, copy=copy)
184 # in pandas we don't store numpy str dtypes, so convert to object
185 if isinstance(dtype, np.dtype) and issubclass(values.dtype.type, str):
File ~/projects/wnt_activate_esti/.venv/lib/python3.13/site-packages/pandas/core/dtypes/astype.py:133, in _astype_nansafe(arr, dtype, copy, skipna)
129 raise ValueError(msg)
131 if copy or arr.dtype == object or dtype == object:
132 # Explicit copy, or required since NumPy can't view from / to object.
--> 133 return arr.astype(dtype, copy=True)
135 return arr.astype(dtype, copy=copy)
ValueError: invalid literal for int() with base 10: '5xFADHEMI'
When run the
pyWGCNA_5xFAD.analyseWGCNA(show=False)Why the official codes have the error?