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But calling pl.dpt on this object yields an error, looking at the above outout of tl.dpt it seems that dpt_groups was not created in adata.obs if n_branchings=0?
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/usr/local/lib/python3.6/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2524 try:
-> 2525 return self._engine.get_loc(key)
2526 except KeyError:
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 'dpt_groups'
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
<ipython-input-102-eb7d1d859c99> in <module>()
----> 1 sc.pl.dpt(adata, groups=None)
~/gitDevelopment/scanpy/scanpy/plotting/tools/__init__.py in dpt(adata, basis, color, alpha, groups, components, projection, legend_loc, legend_fontsize, legend_fontweight, color_map, palette, right_margin, size, title, show, save)
677 """
678 colors = ['dpt_pseudotime']
--> 679 if len(np.unique(adata.obs['dpt_groups'].values)) > 1: colors += ['dpt_groups']
680 if color is not None: colors = color
681 dpt_scatter(
/usr/local/lib/python3.6/site-packages/pandas/core/frame.py in __getitem__(self, key)
2137 return self._getitem_multilevel(key)
2138 else:
-> 2139 return self._getitem_column(key)
2140
2141 def _getitem_column(self, key):
/usr/local/lib/python3.6/site-packages/pandas/core/frame.py in _getitem_column(self, key)
2144 # get column
2145 if self.columns.is_unique:
-> 2146 return self._get_item_cache(key)
2147
2148 # duplicate columns & possible reduce dimensionality
/usr/local/lib/python3.6/site-packages/pandas/core/generic.py in _get_item_cache(self, item)
1840 res = cache.get(item)
1841 if res is None:
-> 1842 values = self._data.get(item)
1843 res = self._box_item_values(item, values)
1844 cache[item] = res
/usr/local/lib/python3.6/site-packages/pandas/core/internals.py in get(self, item, fastpath)
3841
3842 if not isna(item):
-> 3843 loc = self.items.get_loc(item)
3844 else:
3845 indexer = np.arange(len(self.items))[isna(self.items)]
/usr/local/lib/python3.6/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2525 return self._engine.get_loc(key)
2526 except KeyError:
-> 2527 return self._engine.get_loc(self._maybe_cast_indexer(key))
2528
2529 indexer = self.get_indexer([key], method=method, tolerance=tolerance)
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 'dpt_groups'
tl.dpt with no branching events works:
But calling pl.dpt on this object yields an error, looking at the above outout of tl.dpt it seems that dpt_groups was not created in adata.obs if n_branchings=0?
scanpy==1.0.4+11.gc241098 anndata==0.5.10 numpy==1.14.2 scipy==1.0.1 pandas==0.22.0 scikit-learn==0.19.1 statsmodels==0.8.0 python-igraph==0.7.1 louvain==0.6.1
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