Closed rLannes closed 10 months ago
Hi, I have the following issue any idea how to fix, or what the causes?
scf.tl.linearity_deviation(Neutrophile, start_milestone="immature", end_milestone="mature", n_jobs=2, plot=True, basis="X_umap") Estimation of deviation from linearity --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) Input In [29], in <cell line: 1>() ----> 1 scf.tl.linearity_deviation(Neutrophile, 2 start_milestone="immature", 3 end_milestone="mature", 4 n_jobs=2, 5 plot=True, 6 basis="umap") File ~/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scFates/tools/linearity_deviation.py:151, in linearity_deviation(adata, start_milestone, end_milestone, percentiles, n_jobs, n_map, plot, basis, copy) 148 n_jobs_map = n_jobs 149 n_jobs = 1 --> 151 rss = ProgressParallel( 152 total=n_map, 153 n_jobs=n_jobs_map, 154 use_tqdm=n_map > 1, 155 desc=" multi mapping", 156 file=sys.stdout, 157 )(delayed(lindev_map)(m) for m in range(n_map)) 159 if plot: 160 import scanpy as sc File ~/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scFates/tools/utils.py:46, in ProgressParallel.__call__(self, *args, **kwargs) 39 def __call__(self, *args, **kwargs): 40 with tqdm( 41 disable=not self._use_tqdm, 42 total=self._total, 43 desc=self._desc, 44 file=self._file, 45 ) as self._pbar: ---> 46 return Parallel.__call__(self, *args, **kwargs) File ~/.local/lib/python3.9/site-packages/joblib/parallel.py:1863, in Parallel.__call__(self, iterable) 1861 output = self._get_sequential_output(iterable) 1862 next(output) -> 1863 return output if self.return_generator else list(output) 1865 # Let's create an ID that uniquely identifies the current call. If the 1866 # call is interrupted early and that the same instance is immediately 1867 # re-used, this id will be used to prevent workers that were 1868 # concurrently finalizing a task from the previous call to run the 1869 # callback. 1870 with self._lock: File ~/.local/lib/python3.9/site-packages/joblib/parallel.py:1792, in Parallel._get_sequential_output(self, iterable) 1790 self.n_dispatched_batches += 1 1791 self.n_dispatched_tasks += 1 -> 1792 res = func(*args, **kwargs) 1793 self.n_completed_tasks += 1 1794 self.print_progress() File ~/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scFates/tools/linearity_deviation.py:94, in linearity_deviation.<locals>.lindev_map(m) 83 img.add_edges(edges) 85 cells = getpath( 86 img, 87 graph["milestones"][start_milestone], (...) 91 df, 92 ) ---> 94 t_perc = [cells.t.quantile(p / 100) for p in percentiles] 96 df[name + "_lindev_sel"] = np.nan 97 df.loc[ 98 adata.obs_names.isin(cells.index), name + "_lindev_sel" 99 ] = "putative bridge" File ~/mambaforge/envs/scvi-env/lib/python3.9/site-packages/scFates/tools/linearity_deviation.py:94, in <listcomp>(.0) 83 img.add_edges(edges) 85 cells = getpath( 86 img, 87 graph["milestones"][start_milestone], (...) 91 df, 92 ) ---> 94 t_perc = [cells.t.quantile(p / 100) for p in percentiles] 96 df[name + "_lindev_sel"] = np.nan 97 df.loc[ 98 adata.obs_names.isin(cells.index), name + "_lindev_sel" 99 ] = "putative bridge" AttributeError: 'NoneType' object has no attribute 't'
my bad! did something wrong
Hi, I have the following issue any idea how to fix, or what the causes?