The GSM3689776 dataset in the example seems not working with alona

[zhjning]

Hi, as I can run alona successfully with my own data, I find it quite weird that alona failed with the example case. And it seems that GSM3689776 is from mouse rather than human, so I changed the species parameter to mouse, but it still throw out errors when do CTA_RANK_F step. The row values from the same column in the median_expr_Z matrix seems were all the same and ret returns an empty list. Here's the error message showed:

/home/z013/miniconda3/lib/python3.7/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in greater return (a < x) & (x < b) /home/z013/miniconda3/lib/python3.7/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in less return (a < x) & (x < b) /home/z013/miniconda3/lib/python3.7/site-packages/scipy/stats/_distn_infrastructure.py:1827: RuntimeWarning: invalid value encountered in greater_equal cond2 = (x >= np.asarray(_b)) & cond0 /home/z013/miniconda3/lib/python3.7/site-packages/scipy/stats/_distn_infrastructure.py:1912: RuntimeWarning: invalid value encountered in less_equal cond2 = cond0 & (x <= _a) Traceback (most recent call last): File "/home/z013/miniconda3/lib/python3.7/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/z013/miniconda3/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/z013/.local/lib/python3.7/site-packages/alona/main.py", line 9, in main() File "/home/z013/.local/lib/python3.7/site-packages/alona/main.py", line 5, in main run(prog_name='alona.py') File "/home/z013/miniconda3/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(*args, **kwargs) File "/home/z013/miniconda3/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/z013/miniconda3/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/z013/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/z013/.local/lib/python3.7/site-packages/alona/alona.py", line 187, in run alonacell.analysis() File "/home/z013/.local/lib/python3.7/site-packages/alona/cell.py", line 439, in analysis self.CTA_RANK_F(marker_plot=True) File "/home/z013/.local/lib/python3.7/site-packages/alona/celltypes.py", line 177, in CTA_RANK_F _df = pd.DataFrame(ret[k].to_list()) #refactored File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/series.py", line 910, in getitem return self._get_with(key) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/series.py", line 958, in _get_with return self.loc[key] File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 1768, in getitem return self._getitem_axis(maybe_callable, axis=axis) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 1954, in _getitem_axis return self._getitem_iterable(key, axis=axis) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 1595, in _getitem_iterable keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 1547, in _get_listlike_indexer indexer = ax.get_indexer_for(key) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4501, in get_indexer_for return self.get_indexer(target, **kwargs) File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2729, in get_indexer target, method=method, limit=limit, tolerance=tolerance File "/home/z013/miniconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2753, in get_indexer indexer = self._engine.get_indexer(target._ndarray_values) File "pandas/_libs/index.pyx", line 287, in pandas._libs.index.IndexEngine.get_indexer File "pandas/_libs/hashtable_class_helper.pxi", line 1668, in pandas._libs.hashtable.PyObjectHashTable.lookup TypeError: unhashable type: 'dict'