Error encountered when running ov.utils_plot_embedding_celltype

[Zstark11]

ov.utils.plot_embedding_celltype(adata,figsize=None,basis='X_mde_harmony',
                            celltype_key='scsa_celltype_cellmarker-1',
                            title='Cell type',
                            celltype_range=(2,6),
                            embedding_range=(4,10))

report errors:
The number of cell types is too large, please set the figsize parameter

Afterwards, I adjusted the figsize parameter

ov.utils.plot_embedding_celltype(adata,figsize=(12, 8),basis='X_mde_harmony',
                            celltype_key='scsa_celltype_cellmarker-1',
                            title='Cell type',
                            celltype_range=(2,5),
                            embedding_range=(4,10))

report errors:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexes/base.py:3805](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexes/base.py#line=3804), in Index.get_loc(self, key)
   3804 try:
-> 3805     return self._engine.get_loc(casted_key)
   3806 except KeyError as err:

File index.pyx:167, in pandas._libs.index.IndexEngine.get_loc()

File index.pyx:196, in pandas._libs.index.IndexEngine.get_loc()

File pandas/_libs/hashtable_class_helper.pxi:7081, in pandas._libs.hashtable.PyObjectHashTable.get_item()

File pandas/_libs/hashtable_class_helper.pxi:7089, in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'scsa_celltype_cellmarker-1'

The above exception was the direct cause of the following exception:

KeyError                                  Traceback (most recent call last)
Cell In[54], line 1
----> 1 ov.utils.plot_embedding_celltype(adata,figsize=(12, 8),basis='X_mde_harmony',
      2                             celltype_key='scsa_celltype_cellmarker-1',
      3                             title='Cell type',
      4                             celltype_range=(2,5),
      5                             embedding_range=(4,10))

File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/utils/_plot.py:554](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/omicverse/utils/_plot.py#line=553), in plot_embedding_celltype(adata, figsize, basis, celltype_key, title, celltype_range, embedding_range, xlim)
    550 for idx,cell in zip(range(cell_num_pd.shape[0]),
    551                     adata.obs[celltype_key].cat.categories):
    552     ax2.scatter(100,
    553             cell,c=cell_color_dict[cell],s=50)
--> 554     ax2.plot((100,cell_num_pd.loc[cell,celltype_key]),(idx,idx),
    555             c=cell_color_dict[cell],lw=4)
    556     ax2.text(100,idx+0.2,
    557             cell+'('+str("{:,}".format(cell_num_pd.loc[cell,celltype_key]))+')',fontsize=11)
    558 ax2.set_xlim(xlim,cell_num_pd.iloc[1].values[0]) 

File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexing.py:1183](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexing.py#line=1182), in _LocationIndexer.__getitem__(self, key)
   1181     key = tuple(com.apply_if_callable(x, self.obj) for x in key)
   1182     if self._is_scalar_access(key):
-> 1183         return self.obj._get_value(*key, takeable=self._takeable)
   1184     return self._getitem_tuple(key)
   1185 else:
   1186     # we by definition only have the 0th axis

File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/frame.py:4214](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/frame.py#line=4213), in DataFrame._get_value(self, index, col, takeable)
   4211     series = self._ixs(col, axis=1)
   4212     return series._values[index]
-> 4214 series = self._get_item_cache(col)
   4215 engine = self.index._engine
   4217 if not isinstance(self.index, MultiIndex):
   4218     # CategoricalIndex: Trying to use the engine fastpath may give incorrect
   4219     #  results if our categories are integers that dont match our codes
   4220     # IntervalIndex: IntervalTree has no get_loc

File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/frame.py:4638](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/frame.py#line=4637), in DataFrame._get_item_cache(self, item)
   4633 res = cache.get(item)
   4634 if res is None:
   4635     # All places that call _get_item_cache have unique columns,
   4636     #  pending resolution of GH#33047
-> 4638     loc = self.columns.get_loc(item)
   4639     res = self._ixs(loc, axis=1)
   4641     cache[item] = res

File [~/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexes/base.py:3812](http://biotrainee.vip:8102/home/data/miniconda3/envs/ZGY-1/lib/python3.10/site-packages/pandas/core/indexes/base.py#line=3811), in Index.get_loc(self, key)
   3807     if isinstance(casted_key, slice) or (
   3808         isinstance(casted_key, abc.Iterable)
   3809         and any(isinstance(x, slice) for x in casted_key)
   3810     ):
   3811         raise InvalidIndexError(key)
-> 3812     raise KeyError(key) from err
   3813 except TypeError:
   3814     # If we have a listlike key, _check_indexing_error will raise
   3815     #  InvalidIndexError. Otherwise we fall through and re-raise
   3816     #  the TypeError.
   3817     self._check_indexing_error(key)

KeyError: 'scsa_celltype_cellmarker-1'

Checked the contents of scsa_celltype_cellmarker-1 and did not find any abnormalities
adata.obs["scsa_celltype_cellmarker-1"]

AAACCTGAGGAT    Natural killer T (NKT) cell
AAACCTGCAGCG    Natural killer T (NKT) cell
AAACCTGGTACG    Natural killer T (NKT) cell
AAACCTGTCTTT                         T cell
AAACGGGAGCTG                      Stem cell
                           ...             
TTTGTCACAGAT                      Astrocyte
TTTGTCAGTGAT         Neural progenitor cell
TTTGTCAGTTCA                Epithelial cell
TTTGTCATCAAC                        Unknown
TTTGTCATCATA                   TCA                Epithelial cell
TTTGTCATCAAC                        Unknown
TTTGTCATCATA                      Stem cell
Name: scsa_celltype_cellmarker-1, Length: 10317, dtype: category
Categories (11, object): ['Astrocyte', 'B cell', 'Endothelial cell', 'Epithelial cell', ..., 'Neural progenitor cell', 'Stem cell', 'T cell', 'Unknown']   Stem cell
Name: scsa_celltype_cellmarker-1, Length: 10317, dtype: category
Categories (11, object): ['Astrocyte', 'B cell', 'Endothelial cell', 'Epithelial cell', ..., 'Neural progenitor cell', 'Stem cell', 'T cell', 'Unknown']

[Zstark11]

I also reported the same error using SCSA's example data

[GhostInTheShellwjc]

I encounter the same problem with you.It only influences the left part of the picture,and
the umap picture is right.You can draw a pie chart instead of the left part (the sum of cells),using plotly.

[Zstark11]

ov.utils.plot_embedding_celltype

What is the specific code to draw this pie chart? Is it a function in the ov.utils.plot_embedding_celltype?