Zstark11
commented
1 week ago Solved issue: After updating the pandas version from 1.5.3 to 2.2.3, it successfully ran
Open Zstark11 opened 1 week ago
Zstark11
commented
1 week ago Solved issue: After updating the pandas version from 1.5.3 to 2.2.3, it successfully ran
Zstark11
commented
1 week ago The subsequent code also encountered errors
fig,ax1,ax2=v0.plot_trajectory_gams(basis='X_umap',clusters='scsa_celltype_cellmarker-1',draw_all_curves=False)
plt.savefig('via_fig4.pdf',dpi=300,bbox_inches='tight')
plt.show(block=True)0% (0 of 11) | | Elapsed Time: 0:00:00 ETA: --:--:--
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[10], line 1
----> 1 fig,ax1,ax2=v0.plot_trajectory_gams(basis='X_umap',clusters='scsa_celltype_cellmarker-1',draw_all_curves=False)
2 #fig.savefig('figures/via_fig3.png',dpi=300,bbox_inches = 'tight')
3 plt.savefig('via_fig4.pdf',dpi=300,bbox_inches='tight')
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/single/_via.py:330](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/single/_via.py#line=329), in pyVIA.plot_trajectory_gams(self, clusters, basis, via_fine, idx, title_str, draw_all_curves, arrow_width_scale_factor, scatter_size, scatter_alpha, figsize, linewidth, marker_edgewidth, cmap_pseudotime, dpi, highlight_terminal_states, use_maxout_edgelist)
328 self.adata.obs[clusters]=self.adata.obs[clusters].astype('category')
329 embedding=self.adata.obsm[basis]
--> 330 fig,ax1,ax2 = draw_trajectory_gams_pyomic(adata=self.adata,clusters=clusters,via_object=self.model,
331 via_fine=via_fine, embedding=embedding, idx=idx,
332 title_str=title_str, draw_all_curves=draw_all_curves, arrow_width_scale_factor=arrow_width_scale_factor,
333 scatter_size=scatter_size, scatter_alpha=scatter_alpha,figsize=figsize,
334 linewidth=linewidth, marker_edgewidth=marker_edgewidth, cmap_pseudotime=cmap_pseudotime,dpi=dpi,
335 highlight_terminal_states=highlight_terminal_states, use_maxout_edgelist=use_maxout_edgelist)
336 return fig,ax1,ax2
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/single/_via.py:809](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/single/_via.py#line=808), in draw_trajectory_gams_pyomic(adata, clusters, via_object, via_fine, embedding, idx, title_str, draw_all_curves, arrow_width_scale_factor, scatter_size, scatter_alpha, figsize, linewidth, marker_edgewidth, cmap_pseudotime, dpi, highlight_terminal_states, use_maxout_edgelist)
806 y_val = y_val.reshape((len(y_val), -1))
807 xp = np.linspace(minx, maxx, 500)
--> 809 gam50 = pg.LinearGAM(n_splines=4, spline_order=3, lam=10).gridsearch(x_val, y_val)
810 XX = gam50.generate_X_grid(term=0, n=500)
811 preds = gam50.predict(XX)
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py:1894](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py#line=1893), in GAM.gridsearch(self, X, y, weights, return_scores, keep_best, objective, progress, **param_grids)
1892 coef = models[-1].coef_
1893 gam.set_params(coef_=coef, force=True, verbose=False)
-> 1894 gam.fit(X, y, weights)
1896 except ValueError as error:
1897 msg = str(error) + '\non model with param[s:\n](file:///S:/n)' + str(param_grid)
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py:920](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py#line=919), in GAM.fit(self, X, y, weights)
917 self.statistics_['m_features'] = X.shape[1]
919 # optimize
--> 920 self._pirls(X, y, weights)
921 # if self._opt == 0:
922 # self._pirls(X, y, weights)
923 # if self._opt == 1:
924 # self._pirls_naive(X, y)
925 return self
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py:686](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py#line=685), in GAM._pirls(self, X, Y, weights)
669 def _pirls(self, X, Y, weights):
670 """
671 Performs stable PIRLS iterations to estimate GAM coefficients
672
(...)
684 None
685 """
--> 686 modelmat = self._modelmat(X) # build a basis matrix for the GLM
687 n, m = modelmat.shape
689 # initialize GLM coefficients if model is not yet fitted
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py:459](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/pygam.py#line=458), in GAM._modelmat(self, X, term)
437 """
438 Builds a model matrix, B, out of the spline basis for each feature
439
(...)
453 containing model matrix of the spline basis for selected features
454 """
455 X = check_X(X, n_feats=self.statistics_['m_features'],
456 edge_knots=self.edge_knots_, dtypes=self.dtype,
457 features=self.feature, verbose=self.verbose)
--> 459 return self.terms.build_columns(X, term=term)
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/terms.py:1719](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/terms.py#line=1718), in TermList.build_columns(self, X, term, verbose)
1717 columns = []
1718 for term_id in term:
-> 1719 columns.append(self._terms[term_id].build_columns(X, verbose=verbose))
1720 return sp.sparse.hstack(columns, format='csc')
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/terms.py:784](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/terms.py#line=783), in SplineTerm.build_columns(self, X, verbose)
768 """construct the model matrix columns for the term
769
770 Parameters
(...)
780 scipy sparse array with n rows
781 """
782 X[:, self.feature][:, np.newaxis]
--> 784 splines = b_spline_basis(X[:, self.feature],
785 edge_knots=self.edge_knots_,
786 spline_order=self.spline_order,
787 n_splines=self.n_splines,
788 sparse=True,
789 periodic=self.basis in ['cp'],
790 verbose=verbose)
792 if self.by is not None:
793 splines = splines.multiply(X[:, self.by][:, np.newaxis])
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/utils.py:649](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pygam/utils.py#line=648), in b_spline_basis(x, edge_knots, n_splines, spline_order, sparse, periodic, verbose)
646 aug_knots[-1] += 1e-9 # want last knot inclusive
648 # prepare Haar Basis
--> 649 bases = (x >= aug_knots[:-1]).astype(np.int) * \
650 (x < aug_knots[1:]).astype(np.int)
651 bases[-1] = bases[-2][::-1] # force symmetric bases at 0 and 1
653 # do recursion from Hastie et al. vectorized
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/numpy/__init__.py:324](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/numpy/__init__.py#line=323), in __getattr__(attr)
319 warnings.warn(
320 f"In the future `np.{attr}` will be defined as the "
321 "corresponding NumPy scalar.", FutureWarning, stacklevel=2)
323 if attr in __former_attrs__:
--> 324 raise AttributeError(__former_attrs__[attr])
326 if attr == 'testing':
327 import numpy.testing as testing
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecationsDo you need to lower the numpy version to below 1.20.0?
ZHANGDAPA
commented
1 day ago had the same problem
ZHANGDAPA
commented
9 hours ago ImportError Traceback (most recent call last) Cell In[1], line 1 ----> 1 import omicverse as ov
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/init.py:11 8 from pkg_resources import get_distribution 9 version = lambda name: get_distribution(name).version ---> 11 from . import bulk,single,utils,bulk2single,pp,space,pl,externel 12 #usually 13 from .utils._data import read
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/init.py:8 1 r""" 2 bulk (A omic framework for bulk omic analysis) 3 """ 5 #from Pyomic.bulk.DeGene import find_DEG,Density_norm,Plot_gene_expression,ID_mapping 6 #from Pyomic.bulk.Gene_module import pywgcna ----> 8 from ._Gene_module import pyWGCNA,readWGCNA 9 from ._Enrichment import pyGSEA,pyGSE,geneset_enrichment,geneset_plot,geneset_enrichment_GSEA,geneset_plot_multi,enrichment_multi_concat 10 from ._network import pyPPI,string_interaction,string_map,generate_G
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/_Gene_module.py:2 ----> 2 from ._dynamicTree import cutreeHybrid 3 import pandas as pd 4 import matplotlib.pyplot as plt
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/_dynamicTree.py:784 758 results = dict(labels = OrdNumLabs-UnlabeledExist, 759 cores = ordCoreLabels, 760 smallLabels = SmallLabels, (...) 768 RootBranch = RootBranch, isCluster = isCluster, 769 nPoints = nMerge+1)) 771 return(results) --> 784 import pandas as pd 785 import numpy as np 786 from scipy.cluster.hierarchy import to_tree
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/init.py:22 19 del _hard_dependencies, _dependency, _missing_dependencies 21 # numpy compat ---> 22 from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 24 try: 25 from pandas._libs import hashtable as _hashtable, lib as _lib, tslib as _tslib
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/compat/init.py:25 17 from pandas.compat._constants import ( 18 IS64, 19 PY39, (...) 22 PYPY, 23 ) 24 import pandas.compat.compressors ---> 25 from pandas.compat.numpy import ( 26 is_numpy_dev, 27 np_version_under1p21, 28 ) 29 from pandas.compat.pyarrow import ( 30 pa_version_under7p0, 31 pa_version_under8p0, 32 pa_version_under9p0, 33 pa_version_under11p0, 34 ) 37 def set_function_name(f: F, name: str, cls) -> F:
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/compat/numpy/init.py:25 21 np_percentile_argname = "interpolation" 24 if _nlv < Version(_min_numpy_ver): ---> 25 raise ImportError( 26 f"this version of pandas is incompatible with numpy < {_min_numpy_ver}\n" 27 f"your numpy version is {_np_version}.\n" 28 f"Please upgrade numpy to >= {_min_numpy_ver} to use this pandas version" 29 ) 32 all = [ 33 "np", 34 "_np_version", 35 "is_numpy_dev", 36 ]
ImportError: this version of pandas is incompatible with numpy < 1.20.3 your numpy version is 1.19.5. Please upgrade numpy to >= 1.20.3 to use this pandas version
ZHANGDAPA
commented
9 hours ago TypeError Traceback (most recent call last) Cell In[1], line 1 ----> 1 import omicverse as ov
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/init.py:11 8 from pkg_resources import get_distribution 9 version = lambda name: get_distribution(name).version ---> 11 from . import bulk,single,utils,bulk2single,pp,space,pl,externel 12 #usually 13 from .utils._data import read
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/init.py:8 1 r""" 2 bulk (A omic framework for bulk omic analysis) 3 """ 5 #from Pyomic.bulk.DeGene import find_DEG,Density_norm,Plot_gene_expression,ID_mapping 6 #from Pyomic.bulk.Gene_module import pywgcna ----> 8 from ._Gene_module import pyWGCNA,readWGCNA 9 from ._Enrichment import pyGSEA,pyGSE,geneset_enrichment,geneset_plot,geneset_enrichment_GSEA,geneset_plot_multi,enrichment_multi_concat 10 from ._network import pyPPI,string_interaction,string_map,generate_G
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/_Gene_module.py:24 21 from ..utils import pyomic_palette,plot_network 22 import os ---> 24 from ..externel.PyWGCNA.wgcna import pyWGCNA 25 from ..externel.PyWGCNA.utils import readWGCNA 28 class pyWGCNA_old(object):
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/externel/init.py:1 ----> 1 from . import (scSLAT,CEFCON,mofapy2,GNTD,spaceflow,STT, 2 tosica,STAGATE_pyG,STAligner,spatrio,PROST,cytotrace2, 3 GraphST,commot,cnmf,starfysh,scMulan,flowsig,PyWGCNA,CAST,scanorama 4 )
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/externel/CAST/init.py:1 ----> 1 from .main import CAST_STACK, CAST_MARK, CAST_PROJECT 2 from .CAST_Stack import reg_params, region_detect, corr_dist, CAST_STACK_rough 3 from .visualize import kmeans_plot_multiple, plot_mid, dsplot, plot_mid_v2
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/externel/CAST/main.py:2 1 from .CAST_Mark import ----> 2 from .CAST_Stack import 3 from .CAST_Projection import 4 from .utils import
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/externel/CAST/CAST_Stack.py:14 8 from .visualize import add_scale_bar 10 #################### Registration #################### 11 # Parameters class 13 @dataclass ---> 14 class reg_params: 15 dataname : str 16 ### affine
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/externel/CAST/CAST_Stack.py:19, in reg_params() 17 theta_r1 : float = 0 18 theta_r2 : float = 0 ---> 19 d_list : list[float] = field(default_factory=list) 20 translation_params : list[float] = None 21 mirror_t : list[float] = None
TypeError: 'type' object is not subscriptable
Zstark11
commented
9 hours ago When I lowered Numpy to version 1.19.5, omicverse showed an error
ImportError Traceback (most recent call last) Cell In[1], line 1 ----> 1 import omicverse as ov
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/init.py:11 8 from pkg_resources import get_distribution 9 version = lambda name: get_distribution(name).version ---> 11 from . import bulk,single,utils,bulk2single,pp,space,pl,externel 12 #usually 13 from .utils._data import read
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/init.py:8 1 r""" 2 bulk (A omic framework for bulk omic analysis) 3 """ 5 #from Pyomic.bulk.DeGene import find_DEG,Density_norm,Plot_gene_expression,ID_mapping 6 #from Pyomic.bulk.Gene_module import pywgcna ----> 8 from ._Gene_module import pyWGCNA,readWGCNA 9 from ._Enrichment import pyGSEA,pyGSE,geneset_enrichment,geneset_plot,geneset_enrichment_GSEA,geneset_plot_multi,enrichment_multi_concat 重试 错误原因 10 from ._network import pyPPI,string_interaction,string_map,generate_G
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/_Gene_module.py:2 ----> 2 from ._dynamicTree import cutreeHybrid 3 import pandas as pd 4 import matplotlib.pyplot as plt
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/omicverse/bulk/_dynamicTree.py:784 758 results = dict(labels = OrdNumLabs-UnlabeledExist, 759 cores = ordCoreLabels, 760 smallLabels = SmallLabels, (...) 768 RootBranch = RootBranch, isCluster = isCluster, 769 nPoints = nMerge+1)) 771 return(results) --> 784 import pandas as pd 785 import numpy as np 786 from scipy.cluster.hierarchy import to_tree
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/init.py:22 19 del _hard_dependencies, _dependency, _missing_dependencies 21 # numpy compat ---> 22 from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 24 try: 25 from pandas._libs import hashtable as _hashtable, lib as _lib, tslib as _tslib
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/compat/init.py:25 17 from pandas.compat._constants import ( 18 IS64, 19 PY39, (...) 22 PYPY, 23 ) 24 import pandas.compat.compressors ---> 25 from pandas.compat.numpy import ( 26 is_numpy_dev, 27 np_version_under1p21, 28 ) 29 from pandas.compat.pyarrow import ( 30 pa_version_under7p0, 31 pa_version_under8p0, 32 pa_version_under9p0, 33 pa_version_under11p0, 34 ) 37 def set_function_name(f: F, name: str, cls) -> F:
File ~/anaconda3/envs/omicverse3.8/lib/python3.8/site-packages/pandas/compat/numpy/init.py:25 21 np_percentile_argname = "interpolation"21 np_centent_argname ="中间化" 24 if _nlv < Version(_min_numpy_ver): ---> 25 raise ImportError( 26 f"this version of pandas is incompatible with numpy < {_min_numpy_ver}\n" 27 f"your numpy version is {_np_version}.\n" 28 f"Please upgrade numpy to >= {_min_numpy_ver} to use this pandas version" 29 ) 32 all = [ 33 "np", 34 "_np_version", 35 "is_numpy_dev", 36 ]
ImportError: this version of pandas is incompatible with numpy < 1.20.3 your numpy version is 1.19.5. Please upgrade numpy to >= 1.20.3 to use this pandas version
Omicverse need numpy >= 1.20.3
Dask shows that it has been installed
My data contains' duplicated 'and' unspliced 'layers, but there are no layers such as' palantir_pseudotime', 'palantir_diff_potential', 'palantir_branchsprobs_cell_types',' palantir_branchsprobs', 'X_pca' in the example data